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galaxy-dist commit 9cada14f8765: Make VCF (variant call format) a Galaxy datatype and enable very basic VCF support in trackster. VCF datatype is sniffable and can be converted to summary tree and interval index. In trackster, VCF files are represented as single-base pair feature tracks.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1286396635 14400 # Node ID 9cada14f87657b951ccc9a76af5de03263ba72d9 # Parent 75a3e2a75cdaf8872ef3cafd745524dab2872962 Make VCF (variant call format) a Galaxy datatype and enable very basic VCF support in trackster. VCF datatype is sniffable and can be converted to summary tree and interval index. In trackster, VCF files are represented as single-base pair feature tracks. --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -11,6 +11,7 @@ from galaxy import util from cgi import escape from galaxy.datatypes import metadata from galaxy.datatypes.metadata import MetadataElement +import galaxy_utils.sequence.vcf from sniff import * log = logging.getLogger(__name__) @@ -459,3 +460,18 @@ class ElandMulti( Tabular ): def sniff( self, filename ): return False + +class Vcf( Tabular ): + file_ext = 'vcf' + + def sniff( self, filename ): + try: + # If reader can read and parse file, it's VCF. + for line in list( galaxy_utils.sequence.vcf.Reader( open( filename ) ) ): + pass + return True + except: + return False + + def get_track_type( self ): + return "FeatureTrack", {"data": "interval_index", "index": "summary_tree"} --- a/lib/galaxy/visualization/tracks/data/summary_tree.py +++ b/lib/galaxy/visualization/tracks/data/summary_tree.py @@ -19,6 +19,10 @@ class SummaryTreeDataProvider( object ): if st is None: st = summary_tree_from_file( self.dataset.file_name ) CACHE[filename] = st + + # If chrom is not found in blocks, try removing the first three + # characters (e.g. 'chr') and see if that works. This enables the + # provider to handle chrome names defined as chrXXX and as XXX. if chrom in st.chrom_blocks: pass elif chrom[3:] in st.chrom_blocks: --- a/lib/galaxy/visualization/tracks/data/interval_index.py +++ b/lib/galaxy/visualization/tracks/data/interval_index.py @@ -8,6 +8,7 @@ Payload format: [ uid (offset), start, e import pkg_resources; pkg_resources.require( "bx-python" ) from bx.interval_index_file import Indexes from galaxy.datatypes.interval import Bed, Gff +from galaxy.datatypes.tabular import Vcf MAX_VALS = 5000 # only display first MAX_VALS features @@ -18,13 +19,19 @@ class IntervalIndexDataProvider( object def get_data( self, chrom, start, end, **kwargs ): start, end = int(start), int(end) - chrom = str(chrom) source = open( self.original_dataset.file_name ) index = Indexes( self.converted_dataset.file_name ) results = [] count = 0 message = None + # If chrom is not found in indexes, try removing the first three + # characters (e.g. 'chr') and see if that works. This enables the + # provider to handle chrome names defined as chrXXX and as XXX. + chrom = str(chrom) + if chrom not in index.indexes and chrom[3:] in index.indexes: + chrom = chrom[3:] + for start, end, offset in index.find(chrom, start, end): if count >= MAX_VALS: message = "Only the first %s features are being displayed." % MAX_VALS @@ -34,6 +41,7 @@ class IntervalIndexDataProvider( object feature = source.readline().split() payload = [ offset, start, end ] # TODO: can we use column metadata to fill out payload? + # TODO: use function to set payload data if "no_detail" not in kwargs: length = len(feature) if isinstance( self.original_dataset.datatype, Gff ): @@ -58,7 +66,10 @@ class IntervalIndexDataProvider( object block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] blocks = zip(block_sizes, block_starts) payload.append( [ (start + block[1], start + block[1] + block[0]) for block in blocks] ) - + elif isinstance( self.original_dataset.datatype, Vcf ): + # VCF dataset. + payload.append( feature[2] ) # name + results.append(payload) return { 'data': results, 'message': message } --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -111,6 +111,10 @@ <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/><datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/><datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" display_in_upload="true"/> + <datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true"> + <converter file="vcf_to_interval_index_converter.xml" target_datatype="interval_index"/> + <converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + </datatype><datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/><datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true"><converter file="wiggle_to_array_tree_converter.xml" target_datatype="array_tree"/> @@ -285,6 +289,7 @@ <sniffer type="galaxy.datatypes.tabular:Pileup"/><sniffer type="galaxy.datatypes.interval:Interval"/><sniffer type="galaxy.datatypes.tabular:Sam"/> + <sniffer type="galaxy.datatypes.tabular:Vcf"/><!-- Keep this commented until the sniff method in the assembly.py module is fixed to not read the entire file. --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -9,7 +9,7 @@ is redirected to the browser interface, """ -import math, re, logging, glob, pkg_resources +import re, pkg_resources pkg_resources.require( "bx-python" ) from bx.seq.twobit import TwoBitFile @@ -17,7 +17,7 @@ from galaxy import model from galaxy.util.json import to_json_string, from_json_string from galaxy.web.base.controller import * from galaxy.web.framework import simplejson -from galaxy.web.framework.helpers import time_ago, grids +from galaxy.web.framework.helpers import grids from galaxy.util.bunch import Bunch from galaxy.visualization.tracks.data.array_tree import ArrayTreeDataProvider --- /dev/null +++ b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py @@ -0,0 +1,35 @@ +#!/usr/bin/env python + +""" +Convert from VCF file to interval index file. +""" + +from __future__ import division + +import optparse +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +import galaxy_utils.sequence.vcf +from bx.interval_index_file import Indexes + +def main(): + # Read options, args. + parser = optparse.OptionParser() + (options, args) = parser.parse_args() + in_file, out_file = args + + # Do conversion. + index = Indexes() + reader = galaxy_utils.sequence.vcf.Reader( open( in_file ) ) + offset = reader.metadata_len + for vcf_line in reader: + # VCF format provides a chrom and 1-based position for each variant. + # IntervalIndex expects 0-based coordinates. + index.add( vcf_line.chrom, vcf_line.pos-1, vcf_line.pos, offset ) + offset += len( vcf_line.raw_line ) + + index.write( open( out_file, "w" ) ) + +if __name__ == "__main__": + main() + --- /dev/null +++ b/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.xml @@ -0,0 +1,14 @@ +<tool id="CONVERTER_vcf_to_summary_tree_0" name="Convert VCF to Summary Tree" version="1.0.0" hidden="true"> + <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> + <command interpreter="python">vcf_to_summary_tree_converter.py $input1 $output1</command> + <inputs> + <page> + <param format="vcf" name="input1" type="data" label="Choose VCF file"/> + </page> + </inputs> + <outputs> + <data format="summary_tree" name="output1"/> + </outputs> + <help> + </help> +</tool> --- /dev/null +++ b/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.py @@ -0,0 +1,30 @@ +#!/usr/bin/env python + +""" +Convert from VCF file to summary tree file. + +usage: %prog in_file out_file +""" +from __future__ import division + +import optparse +import galaxy_utils.sequence.vcf +from galaxy.visualization.tracks.summary import SummaryTree + +def main(): + # Read options, args. + parser = optparse.OptionParser() + (options, args) = parser.parse_args() + in_file, out_file = args + + # Do conversion. + st = SummaryTree(block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30) + for line in list( galaxy_utils.sequence.vcf.Reader( open( in_file ) ) ): + # VCF format provides a chrom and 1-based position for each variant. + # SummaryTree expects 0-based coordinates. + st.insert_range( line.chrom, long( line.pos-1 ), long( line.pos ) ) + + st.write(out_file) + +if __name__ == "__main__": + main() --- /dev/null +++ b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml @@ -0,0 +1,14 @@ +<tool id="CONVERTER_vcf_to_interval_index_0" name="Convert VCF to Interval Index" version="1.0.0" hidden="true"> + <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> + <command interpreter="python">vcf_to_interval_index_converter.py $input1 $output1</command> + <inputs> + <page> + <param format="vcf" name="input1" type="data" label="Choose VCF file"/> + </page> + </inputs> + <outputs> + <data format="interval_index" name="output1"/> + </outputs> + <help> + </help> +</tool> --- a/lib/galaxy_utils/sequence/vcf.py +++ b/lib/galaxy_utils/sequence/vcf.py @@ -23,6 +23,8 @@ class VariantCall33( VariantCall ): required_header_length = len( required_header_fields ) def __init__( self, vcf_line, metadata, sample_names ): + # Raw line is needed for indexing file. + self.raw_line = vcf_line self.line = vcf_line.rstrip( '\n\r' ) self.metadata = metadata self.sample_names = sample_names @@ -59,10 +61,14 @@ class Reader( object ): self.vcf_file = fh self.metadata = {} self.header_fields = None + self.metadata_len = 0 self.sample_names = [] self.vcf_class = None + + # Read file metadata. while True: line = self.vcf_file.readline() + self.metadata_len += len( line ) assert line, 'Invalid VCF file provided.' line = line.rstrip( '\r\n' ) if self.vcf_class and line.startswith( self.vcf_class.header_startswith ):

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galaxy-dist commit 75a3e2a75cda: Add support for displaying BAM files at Ensembl
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User chapmanb # Date 1286377408 14400 # Node ID 75a3e2a75cdaf8872ef3cafd745524dab2872962 # Parent a89b59ecb9e06778ee39f0b1b2aed38613c127b6 Add support for displaying BAM files at Ensembl --- a/tool-data/shared/ensembl/ensembl_sites.txt +++ b/tool-data/shared/ensembl/ensembl_sites.txt @@ -2,3 +2,4 @@ #http://www.ensembl.org/info/docs/webcode/linking.html ensembl_Current Current http://www.ensembl.org/ hg19,felCat3,galGal3,bosTau4,canFam2,loxAfr3,cavPor3,equCab2,anoCar1,oryLat2,mm9,monDom5,ponAbe2,susScr2,ornAna1,oryCun2,rn4,rheMac2,gasAcu1,tetNig2,xenTro2,taeGut1,danRer5,ci2,dm3,ce6,sacCer2 Homo_sapiens,Felis_catus,Gallus_gallus,Bos_taurus,Canis_familiaris,Loxodonta_africana,Cavia_porcellus,Equus_caballus,Anolis_carolinensis,Oryzias_latipes,Mus_musculus,Monodelphis_domestica,Pongo_pygmaeus,Sus_scrofa,Ornithorhynchus_anatinus,Oryctolagus_cuniculus,Rattus_norvegicus,Macaca_mulatta,Gasterosteus_aculeatus,Tetraodon_nigroviridis,Xenopus_tropicalis,Taeniopygia_guttata,Danio_rerio,Ciona_intestinalis,Drosophila_melanogaster,Caenorhabditis_elegans,Saccharomyces_cerevisiae ensembl_May_2009 May 2009 http://may2009.archive.ensembl.org/ hg18 Homo_sapiens +ensembl_plants Plants http://plants.ensembl.org/ araTha_tair9 Arabidopsis_thaliana --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -8,6 +8,7 @@ <converter file="bam_to_bai.xml" target_datatype="bai"/><converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree" depends_on="bai"/><display file="ucsc/bam.xml" /> + <display file="ensembl/ensembl_bam.xml" /></datatype><datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true"><converter file="bed_to_gff_converter.xml" target_datatype="gff"/> --- /dev/null +++ b/display_applications/ensembl/ensembl_bam.xml @@ -0,0 +1,25 @@ +<display id="ensembl_bam" version="1.0.0" name="display at Ensembl"> +  +  + <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1"> + +  + <dynamic_param name="site_id" value="0"/> + <dynamic_param name="site_name" value="1"/> + <dynamic_param name="site_link" value="2"/> + <dynamic_param name="site_dbkeys" value="3" split="True" separator="," /> + <dynamic_param name="site_organisms" value="4" split="True" separator="," /> + +  + <filter>${dataset.dbkey in $site_dbkeys}</filter> + +  + <url>${site_link}${site_organism}/Location/View?contigviewbottom=bam:${bam_file.qp}=normal</url> + + <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" /> + <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /> + <param type="template" name="site_organism" strip="True" > + $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] + </param> + </dynamic_links> +</display>

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galaxy-dist commit 7b431b0dbc68: Fixed broken indentation.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Richard Burhans <burhans(a)bx.psu.edu> # Date 1285872631 14400 # Node ID 7b431b0dbc687c1496ef5fba92dd443476d61d60 # Parent 51aaa9eac8182b25dbbffd1de902b78c916cb0f5 Fixed broken indentation. --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -646,10 +646,10 @@ class TwillTestCase( unittest.TestCase ) s2 = os.path.getsize(local_name) if abs(s1-s2) > int(delta): raise Exception, 'Files %s=%db but %s=%db - compare (delta=%s) failed' % (temp_name,s1,local_name,s2,delta) - else: - raise Exception, 'Unimplemented Compare type: %s' % compare - if extra_files: - self.verify_extra_files_content( extra_files, elem.get( 'id' ) ) + else: + raise Exception, 'Unimplemented Compare type: %s' % compare + if extra_files: + self.verify_extra_files_content( extra_files, elem.get( 'id' ) ) except AssertionError, err: errmsg = 'History item %s different than expected, difference (using %s):\n' % ( hid, compare ) errmsg += str( err )

1 0

galaxy-dist commit e32d77e1f47b: Make links in split menubuttons take the link instead of popping up the menu options. Use new menubutton style in data libraries and sharing_base.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1286147560 14400 # Node ID e32d77e1f47b1fc94b3e7511094e4b0d760f1e97 # Parent ba6f40c5b3d3ee82aa6719f98f58d4285bcbd66d Make links in split menubuttons take the link instead of popping up the menu options. Use new menubutton style in data libraries and sharing_base. --- a/templates/sharing_base.mako +++ b/templates/sharing_base.mako @@ -241,8 +241,7 @@ <% user = association.user %><tr><td> - ${user.email} - <a id="user-${i}-popup" class="popup-arrow" style="display: none;">▼</a> + <div class="menubutton popup" id="user-${i}-popup">${user.email}</div></td><td><div popupmenu="user-${i}-popup"> --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div 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f(k===undefined){k={}}k[j]=true;$.jStore.store("history_expand_state",k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStore.store("history_expand_state");if(h===undefined){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStore.store("history_expand_state",h)}).show()};if(a){b()}else{$.jStore.init("galaxy");$.jStore.engineReady(function(){b()})}}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length==0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrappe r"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(".trackster-add").live("click",function(){var b=this,a=$(this);$.ajax({url:a.attr("data- url"),dataType:"html",error:function(){alert("Could not add this dataset to browser.")},success:function(c){var d=window.parent;d.show_modal("Add to Browser:",c,{"Insert into selected":function(){$(d.document).find("input[name=id]:checked").each(function(){var e=$(this).val();d.location=a.attr("action-url")+"&id="+e})},"Insert into new browser":function(){d.location=a.attr("new-url")},Cancel:function(){d.hide_modal()}})}})});$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus();replace_big_select_inputs(20,1500)}); --- a/templates/library/common/browse_library.mako +++ b/templates/library/common/browse_library.mako @@ -50,7 +50,7 @@ <%def name="grid_javascripts()"><script type="text/javascript"> - $( document ).ready( function () { + $(function () { $("#library-grid").each( function() { // Recursively fill in children and descendents of each row var process_row = function( q, parents ) { @@ -70,7 +70,7 @@ // remembering folder states, we'll need something // more sophisticated here. var visible = false; - $(q).find( "span.expandLink").click( function() { + var expand_fn = function() { if ( visible ) { descendents.hide(); descendents.removeClass( "expanded" ); @@ -81,7 +81,9 @@ q.addClass( "expanded" ); visible = true; } - }); + }; + $(q).find("span.expandLink").click(expand_fn); + $(q).find("span.expandLink a").click(expand_fn); // Check/uncheck boxes in subfolders. q.children( "td" ).children( "input[type=checkbox]" ).click( function() { if ( $(this).is(":checked") ) { @@ -103,6 +105,17 @@ }); }); }); + + // For view info links, use a modal popup + /*$(".view-info").live("click", function() { + $.get( $(this).attr("href"), function(info) { + show_modal("View Information", info, { + "Close": function() { hide_modal(); } + }); + }); + return false; + });*/ + function checkForm() { if ( $("select#action_on_datasets_select option:selected").text() == "delete" ) { if ( confirm( "Click OK to delete these datasets?" ) ) { @@ -198,55 +211,56 @@ %endif id="libraryItem-${ldda.id}"><td style="padding-left: ${pad+20}px;"> + <input style="float: left;" type="checkbox" name="ldda_ids" value="${trans.security.encode_id( ldda.id )}" %if selected: - <input type="checkbox" name="ldda_ids" value="${trans.security.encode_id( ldda.id )}" checked/> - %else: - <input type="checkbox" name="ldda_ids" value="${trans.security.encode_id( ldda.id )}"/> + checked="checked" %endif + /> %if ldda.library_dataset.deleted: <span class="libraryItem-error"> - %endif - <a href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">${ldda.name[:50]}</a> - %if ldda.library_dataset.deleted: - </span> - %endif - %if not library.deleted: - <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="dataset-${ldda.id}-popup"> - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify: - <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> - %else: - <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify and not info_association: - <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify and info_association: - <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> - <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_manage: - %if not trans.app.security_agent.dataset_is_public( ldda.dataset ): - <a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='ldda', id=trans.security.encode_id( ldda.dataset.id ), use_panels=use_panels, show_deleted=show_deleted )}">Make public</a> - %endif - <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify: - <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), replace_id=trans.security.encode_id( library_dataset.id ), show_deleted=show_deleted )}">Upload a new version of this dataset</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ldda.has_data: - <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='import_to_history', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a> - <a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels )}">Download this dataset</a> - %endif - %if can_modify: - %if not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.deleted: - <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Delete this dataset</a> - %elif not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.purged and ldda.library_dataset.deleted: - <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Undelete this dataset</a> - %endif - %endif - </div> - %endif + %endif + <div style="float: left; margin-left: 1px;" class="menubutton split popup" id="dataset-${ldda.id}-popup"> + <a class="view-info" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">${ldda.name[:50]}</a> + </div> + %if ldda.library_dataset.deleted: + </span> + %endif + %if not library.deleted: + <div popupmenu="dataset-${ldda.id}-popup"> + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify: + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> + %else: + <a class="action-button" class="view-info" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify and not info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify and info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_manage: + %if not trans.app.security_agent.dataset_is_public( ldda.dataset ): + <a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='ldda', id=trans.security.encode_id( ldda.dataset.id ), use_panels=use_panels, show_deleted=show_deleted )}">Make public</a> + %endif + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify: + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), replace_id=trans.security.encode_id( library_dataset.id ), show_deleted=show_deleted )}">Upload a new version of this dataset</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ldda.has_data: + <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='import_to_history', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels )}">Download this dataset</a> + %endif + %if can_modify: + %if not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.deleted: + <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Delete this dataset</a> + %elif not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.purged and ldda.library_dataset.deleted: + <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Undelete this dataset</a> + %endif + %endif + </div> + %endif </td><td id="libraryItemInfo">${render_library_item_info( ldda )}</td><td>${uploaded_by}</td> @@ -266,12 +280,12 @@ if root_folder: pad = folder_pad - expander = "/static/images/silk/resultset_bottom.png" - folder_img = "/static/images/silk/folder_page.png" + expander = h.url_for("/static/images/silk/resultset_bottom.png") + folder_img = h.url_for("/static/images/silk/folder_page.png") else: pad = folder_pad + 20 - expander = "/static/images/silk/resultset_next.png" - folder_img = "/static/images/silk/folder.png" + expander = h.url_for("/static/images/silk/resultset_next.png") + folder_img = h.url_for("/static/images/silk/folder.png") if created_ldda_ids: created_ldda_ids = util.listify( created_ldda_ids ) if str( folder.id ) in hidden_folder_ids: @@ -311,14 +325,16 @@ %if folder.deleted: <span class="libraryItem-error"> %endif - <span class="expandLink"><span class="rowIcon"></span><a style="margin-left: 5px;" href="javascript:void(0);">${folder.name}</a></span> + <span class="expandLink"><span class="rowIcon"></span> + <div style="float: left; margin-left: 2px;" class="menubutton split popup" id="folder_img-${folder.id}-popup"> + <a href="javascript:void(0);">${folder.name}</a> + </div> %if folder.deleted: </span> %endif %if not branch_deleted( folder ): %if not library.deleted: - <a id="folder_img-${folder.id}-popup" class="popup-arrow" style="display: none;">▼</a><div popupmenu="folder_img-${folder.id}-popup"> %if not branch_deleted( folder ) and can_add: <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add datasets</a> @@ -328,7 +344,7 @@ %if can_modify: <a class="action-button" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> %else: - <a class="action-button" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> + <a class="action-button" class="view-info" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> %endif %endif %if not branch_deleted( folder ) and can_modify and not info_association: --- a/static/june_2007_style/blue/library.css +++ b/static/june_2007_style/blue/library.css @@ -13,7 +13,7 @@ pre.peek{background:white;color:black;wi pre.peek th{color:white;background:#023858;} span.expandLink{padding-left:20px;display:inline-block;vertical-align:middle;background:url(../images/silk/resultset_next.png) no-repeat;} .folderRow.expanded span.expandLink{background:url(../images/silk/resultset_bottom.png) no-repeat;} -.folderRow span.rowIcon{width:16px;height:16px;display:inline-block;vertical-align:middle;background:url(../images/silk/folder.png);} +.folderRow span.rowIcon{float:left;width:16px;height:16px;display:inline-block;vertical-align:middle;background:url(../images/silk/folder.png);} .libraryItem-error{margin-right:2px;padding:0 2px 0 2px;border:1px solid #AA6666;background:#FFCCCC;} .libraryItem-queued{margin-right:2px;padding:0 2px 0 2px;border:1px solid #888888;background:#EEEEEE;} .libraryItem-running{margin-right:2px;padding:0 2px 0 2px;border:1px solid #AAAA66;background:#FFFFCC;} --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -43,7 +43,7 @@ function attach_popupmenu( button_elemen $("#popup-helper").unbind( "click.popupmenu" ).hide(); // $(document).unbind( "click.popupmenu" ); }; - var click = function( e ) { + var click_handler = function( e ) { // var o = $(button_element).offset(); $("#popup-helper").bind( "click.popupmenu", clean ).show(); // $(document).bind( "click.popupmenu", clean ); @@ -62,7 +62,7 @@ function attach_popupmenu( button_elemen } ); return false; }; - $( button_element ).click( click ); + $(button_element).bind("click", click_handler); } function make_popupmenu( button_element, options ) { @@ -112,6 +112,10 @@ function make_popup_menus() { }; }); var b = $( "#" + $(this).attr( 'popupmenu' ) ); + b.find("a").bind("click", function(e) { + e.stopPropagation(); // Stop bubbling so clicking on the link goes through + return true; + }); make_popupmenu( b, options ); $(this).remove(); b.addClass( "popup" ).show(); --- a/static/june_2007_style/library.css.tmpl +++ b/static/june_2007_style/library.css.tmpl @@ -76,6 +76,7 @@ span.expandLink { } .folderRow span.rowIcon { + float: left; width: 16px; height: 16px; display: inline-block; --- a/templates/library/common/library_info.mako +++ b/templates/library/common/library_info.mako @@ -34,9 +34,10 @@ <div class="toolForm"><div class="toolFormTitle"> - <a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}"><b>${library.name[:50]}</b></a> + <div class="menubutton split popup" id="library-${library.id}-popup"> + <a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">${library.name[:50]}</a> + </div> %if can_add or can_modify or can_manage: - <a id="library-${library.id}-popup" class="popup-arrow" style="display: none;">▼</a><div popupmenu="library-${library.id}-popup"> %if not library.deleted: %if can_add and not library.info_association: --- a/templates/library/common/ldda_info.mako +++ b/templates/library/common/ldda_info.mako @@ -46,9 +46,8 @@ <div class="toolForm"><div class="toolFormTitle"> - Information about ${ldda.name} + Information about <div class="menubutton popup" id="dataset-${ldda.id}-popup">${ldda.name}</div> %if not library.deleted and not branch_deleted( ldda.library_dataset.folder ) and not ldda.library_dataset.deleted: - <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a><div popupmenu="dataset-${ldda.id}-popup"> %if can_modify: <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a>

1 0

galaxy-dist commit ba6f40c5b3d3: Refactored refresh_on_change javascript code to run in galaxy.base when the page is loaded. Fixed bug with autocomplete_select: when switching from a value within refresh_on_change_values to a value outside of it, the page did not refresh. Removed duplicate code from templates.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1285964434 14400 # Node ID ba6f40c5b3d3ee82aa6719f98f58d4285bcbd66d # Parent 4990d7b95b7273ba7159bfb2db1931a4e74a980a Refactored refresh_on_change javascript code to run in galaxy.base when the page is loaded. Fixed bug with autocomplete_select: when switching from a value within refresh_on_change_values to a value outside of it, the page did not refresh. Removed duplicate code from templates. --- a/templates/requests/common/new_request.mako +++ b/templates/requests/common/new_request.mako @@ -5,31 +5,6 @@ ${render_msg( message, status )} %endif -<script type="text/javascript"> -$( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#new_request" ).submit(); - } - }); -}); -</script> - <%def name="javascripts()"> ${parent.javascripts()} ${h.js("jquery.autocomplete", "autocomplete_tagging" )} --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -9,30 +9,6 @@ <%def name="javascripts()"> ${parent.javascripts()} - <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#registration" ).submit(); - } - }); - }); - </script></%def><% --- a/templates/library/common/folder_info.mako +++ b/templates/library/common/folder_info.mako @@ -4,30 +4,6 @@ <%def name="javascripts()"> ${parent.javascripts()} - <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#edit_info" ).submit(); - } - }); - }); - </script></%def><% --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var 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m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!=""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();retur n})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStore.store("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStore.remove("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id;var h=$(this).children("div.historyItemBody");var i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){var k=$.jStore.store("history_expand_state");if(k){delete k[j];$.jStore.store("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){var k=$.jStore.store("history_expand_state");if(k===undefined){k={}}k[j]=true;$.jStore.store("history_expand_state" ,k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStore.store("history_expand_state");if(h===undefined){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStore.store("history_expand_state",h)}).show()};if(a){b()}else{$.jStore.init("galaxy");$.jStore.engineReady(function(){b()})}}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length==0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(t his).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}function GalaxyAsync(a){this.url_dict={};this.log_action=(a===undefined?false:a)}GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(".trackster-add").live("click",function(){var b=this,a=$(this);$.ajax({url:a.attr("data-url"),dataType:"html",error:function(){alert("Could not add this dataset t o browser.")},success:function(c){var d=window.parent;d.show_modal("Add to Browser:",c,{"Insert into selected":function(){$(d.document).find("input[name=id]:checked").each(function(){var e=$(this).val();d.location=a.attr("action-url")+"&id="+e})},"Insert into new browser":function(){d.location=a.attr("new-url")},Cancel:function(){d.hide_modal()}})}})});$(document).ready(function(){$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus();replace_big_select_inputs(20,1500)}); +function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return fa lse};$(b).click(c)}function make_popupmenu(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");if(obj_length(b)<=0){$("<li/>").html("No options").appendTo(a)}$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d)}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function naturalSort(i,g){var n=/(-?[0-9\.]+)/g,j=i.toString().toLowerCase()||"",f= g.toString().toLowerCase()||"",k=String.fromCharCode(0),l=j.replace(n,k+"$1"+k).split(k),e=f.replace(n,k+"$1"+k).split(k),d=(new Date(j)).getTime(),m=d?(new Date(f)).getTime():null;if(m){if(d<m){return -1}else{if(d>m){return 1}}}for(var h=0,c=Math.max(l.length,e.length);h<c;h++){oFxNcL=parseFloat(l[h])||l[h];oFyNcL=parseFloat(e[h])||e[h];if(oFxNcL<oFyNcL){return -1}else{if(oFxNcL>oFyNcL){return 1}}}return 0}function replace_big_select_inputs(a,b){if(!jQuery().autocomplete){return}if(a===undefined){a=20}if(b===undefined){b=3000}$("select").each(function(){var d=$(this);var g=d.find("option").length;if((g<a)||(g>b)){return}if(d.attr("multiple")==true){return}if(d.hasClass("no-autocomplete")){return}var m=d.attr("value");var c=$("<input type='text' class='text-and-autocomplete-select'></input>");c.attr("size",40);c.attr("name",d.attr("name"));c.attr("id",d.attr("id"));c.click(function(){var n=$(this).val();$(this).val("Loading...");$(this).showAllInCache();$(this).val(n);$(this ).select()});var e=[];var i={};d.children("option").each(function(){var o=$(this).text();var n=$(this).attr("value");e.push(o);i[o]=n;i[n]=n;if(n==m){c.attr("value",o)}});if(m==""||m=="?"){c.attr("value","Click to Search or Select")}if(d.attr("name")=="dbkey"){e=e.sort(naturalSort)}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:b,minChars:0,hideForLessThanMinChars:false};c.autocomplete(e,f);d.replaceWith(c);var k=function(){var o=c.attr("value");var n=i[o];if(n!==null&&n!==undefined){c.attr("value",n)}else{if(m!=""){c.attr("value",m)}else{c.attr("value","?")}}};c.parents("form").submit(function(){k()});$(document).bind("convert_dbkeys",function(){k()});if(d.attr("refresh_on_change")=="true"){var h=d.attr("refresh_on_change_values"),l=d.attr("last_selected_value");if(h!==undefined){h=h.split(",")}var j=function(){var n=i[c.attr("value")];if(n!==null&&n!==undefined){if($.inArray(n,h)===-1&&$.inArray(l,h)===-1){return}c.attr("value",n);$(window). trigger("refresh_on_change");c.parents("form").submit()}};c.bind("result",j);c.keyup(function(n){if(n.keyCode===13){j()}});c.keydown(function(n){if(n.keyCode===13){return false}})}})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!=""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}funct ion init_history_items(d,a,c){var b=function(){try{var e=$.jStore.store("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStore.remove("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id;var h=$(this).children("div.historyItemBody");var i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){var k=$.jStore.store("history_expand_state");if(k){delete k[j];$.jStore.store("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){var k=$.jStore.store("history_expand_state");if(k===undefined){k={}}k[j]=true;$.jStore.store("history_expand_state",k)}}retu rn false})});$("#top-links > a.toggle").click(function(){var h=$.jStore.store("history_expand_state");if(h===undefined){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStore.store("history_expand_state",h)}).show()};if(a){b()}else{$.jStore.init("galaxy");$.jStore.engineReady(function(){b()})}}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length==0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show ()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(".trackster-add").live("click",function(){var b=this,a=$(this);$.ajax({url:a.attr("data-url"),dataType:"html",error:function(){alert("Could not add this dataset to br owser.")},success:function(c){var d=window.parent;d.show_modal("Add to Browser:",c,{"Insert into selected":function(){$(d.document).find("input[name=id]:checked").each(function(){var e=$(this).val();d.location=a.attr("action-url")+"&id="+e})},"Insert into new browser":function(){d.location=a.attr("new-url")},Cancel:function(){d.hide_modal()}})}})});$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus();replace_big_select_inputs(20,1500)}); --- a/templates/library/common/library_info.mako +++ b/templates/library/common/library_info.mako @@ -4,30 +4,6 @@ <%def name="javascripts()"> ${parent.javascripts()} - <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#edit_info" ).submit(); - } - }); - }); - </script></%def><% --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -13,43 +13,24 @@ from galaxy.util.expressions import Expr ${h.css( "base", "autocomplete_tagging" )} ${h.js( "jquery", "galaxy.base", "jquery.autocomplete" )} <script type="text/javascript"> -$( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } +$(function() { + $(window).bind("refresh_on_change", function() { + $(':file').each( function() { + var file = $(this); + var file_value = file.val(); + if (file_value) { + // disable file input, since we don't want to upload the file on refresh + var file_name = $(this).attr("name"); + file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } ); + // create a new hidden field which stores the filename and has the original name of the file input + var new_file_input = $('<input type="hidden" />'); + new_file_input.attr( { "value": file_value, "name": file_name } ); + file.after(new_file_input); } - } - else { - refresh = true; - } - if ( refresh ){ - $( ':file' ).each( function() { - var file_value = $( this )[0].value; - if ( file_value ) { - //disable file input, since we don't want to upload the file on refresh - var file_name = $( this )[0].name; - $( this )[0].name = 'replaced_file_input_' + file_name - $( this )[0].disable = true; - //create a new hidden field which stores the filename and has the original name of the file input - var new_file_input = document.createElement( 'input' ); - new_file_input.type = 'hidden'; - new_file_input.value = file_value; - new_file_input.name = file_name; - document.getElementById( 'tool_form' ).appendChild( new_file_input ); - } - } ); - $( "#tool_form" ).submit(); - } - }); + }); + }); }); + %if not add_frame.debug: if( window.name != "galaxy_main" ) { location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' ); --- a/templates/requests/common/find.mako +++ b/templates/requests/common/find.mako @@ -5,31 +5,6 @@ ${render_msg( message, status )} %endif -<script type="text/javascript"> -$( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#find_request" ).submit(); - } - }); -}); -</script> - <%def name="javascripts()"> ${parent.javascripts()} ${h.js("jquery.autocomplete", "autocomplete_tagging" )} --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -119,7 +119,7 @@ function make_popup_menus() { } // Alphanumeric/natural sort fn -function naturalSort(a, b){ +function naturalSort(a, b) { // setup temp-scope variables for comparison evauluation var re = /(-?[0-9\.]+)/g, x = a.toString().toLowerCase() || '', @@ -249,45 +249,24 @@ function replace_big_select_inputs(min_l $(document).bind("convert_dbkeys", function() { submit_hook(); } ); // If select is refresh on change, mirror this behavior. - if (select_elt.attr('refresh_on_change') == 'true') - { + if (select_elt.attr('refresh_on_change') == 'true') { // Get refresh vals. - var refresh_vals = select_elt.attr('refresh_on_change_values'); - if (refresh_vals !== undefined) - refresh_vals = refresh_vals.split(","); - + var ref_on_change_vals = select_elt.attr('refresh_on_change_values'), + last_selected_value = select_elt.attr("last_selected_value"); + if (ref_on_change_vals !== undefined) + ref_on_change_vals = ref_on_change_vals.split(','); + // Function that attempts to refresh based on the value in the text element. - var try_refresh_fn = function() - { - // - // If value entered can be matched to value, do so and refresh by submitting parent form. - // - + var try_refresh_fn = function() { // Get new value and see if it can be matched. - var cur_value = text_input_elt.attr('value'); - var new_value = select_mapping[cur_value]; - if (new_value !== null && new_value !== undefined) - { - // Do refresh if new value is refresh value or if there are no refresh values. - refresh = false; - if (refresh_vals !== undefined) - { - for (var i= 0; i < refresh_vals.length; i++ ) - if (new_value == refresh_vals[i]) - { - refresh = true; - break; - } + var new_value = select_mapping[text_input_elt.attr('value')]; + if (new_value !== null && new_value !== undefined) { + if ($.inArray(new_value, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + return; } - else - // Refresh for all values. - refresh = true; - - if (refresh) - { - text_input_elt.attr('value', new_value); - text_input_elt.parents('form').submit(); - } + text_input_elt.attr('value', new_value); + $(window).trigger("refresh_on_change"); + text_input_elt.parents('form').submit(); } }; @@ -295,15 +274,17 @@ function replace_big_select_inputs(min_l // case a user may have manually entered a value that needs to be refreshed). text_input_elt.bind("result", try_refresh_fn); text_input_elt.keyup( function(e) { - if ( e.keyCode === 13 ) // Return key + if (e.keyCode === 13) { // Return key try_refresh_fn(); + } }); - // Disable return key so that it does not submit the form automatically. This is done because elememnt should behave like a + // Disable return key so that it does not submit the form automatically. This is done because element should behave like a // select (enter = select), not text input (enter = submit form). text_input_elt.keydown( function(e) { - if ( e.keyCode === 13 ) // Return key + if (e.keyCode === 13) { // Return key return false; + } }); } }); @@ -482,13 +463,13 @@ function commatize( number ) { } // Reset tool search to start state. -function reset_tool_search( initValue ) -{ +function reset_tool_search( initValue ) { // Function may be called in top frame or in tool_menu_frame; // in either case, get the tool menu frame. var tool_menu_frame = $("#galaxy_tools").contents(); - if (tool_menu_frame.length == 0) + if (tool_menu_frame.length == 0) { tool_menu_frame = $(document); + } // Remove classes that indicate searching is active. $(this).removeClass("search_active"); @@ -499,18 +480,18 @@ function reset_tool_search( initValue ) tool_menu_frame.find(".toolTitle").show(); tool_menu_frame.find(".toolPanelLabel").show(); tool_menu_frame.find(".toolSectionWrapper").each( function() { - if ($(this).attr('id') != 'recently_used_wrapper') + if ($(this).attr('id') != 'recently_used_wrapper') { // Default action. $(this).show(); - else if ($(this).hasClass("user_pref_visible")) + } else if ($(this).hasClass("user_pref_visible")) { $(this).show(); + } }); tool_menu_frame.find("#search-no-results").hide(); // Reset search input. tool_menu_frame.find("#search-spinner").hide(); - if (initValue) - { + if (initValue) { var search_input = tool_menu_frame.find("#tool-search-query"); search_input.val("search tools"); search_input.css("font-style", "italic"); @@ -518,20 +499,17 @@ function reset_tool_search( initValue ) } // Create GalaxyAsync object. -function GalaxyAsync(log_action) -{ +var GalaxyAsync = function(log_action) { this.url_dict = {}; this.log_action = (log_action === undefined ? false : log_action); } -GalaxyAsync.prototype.set_func_url = function( func_name, url ) -{ - this.url_dict[func_name] = url; +GalaxyAsync.prototype.set_func_url = function( func_name, url ) { + this.url_dict[func_name] = url; }; // Set user preference asynchronously. -GalaxyAsync.prototype.set_user_pref = function( pref_name, pref_value ) -{ +GalaxyAsync.prototype.set_user_pref = function( pref_name, pref_value ) { // Get URL. var url = this.url_dict[arguments.callee]; if (url === undefined) { return false; } @@ -544,8 +522,7 @@ GalaxyAsync.prototype.set_user_pref = fu }; // Log user action asynchronously. -GalaxyAsync.prototype.log_user_action = function( action, context, params ) -{ +GalaxyAsync.prototype.log_user_action = function( action, context, params ) { if (!this.log_action) { return; } // Get URL. @@ -588,7 +565,24 @@ GalaxyAsync.prototype.log_user_action = }); + $(document).ready( function() { + $("select[refresh_on_change='true']").change( function() { + var select_field = $(this), + select_val = select_field.val(), + refresh = false, + ref_on_change_vals = select_field.attr("refresh_on_change_values"); + if (ref_on_change_vals) { + ref_on_change_vals = ref_on_change_vals.split(','); + var last_selected_value = select_field.attr("last_selected_value"); + if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + return; + } + } + $(window).trigger("refresh_on_change"); + select_field.get(0).form.submit(); + }); + // Links with confirmation $( "a[confirm]" ).click( function() { return confirm( $(this).attr("confirm") ); --- a/templates/requests/common/edit_request.mako +++ b/templates/requests/common/edit_request.mako @@ -5,31 +5,6 @@ ${render_msg( message, status )} %endif -<script type="text/javascript"> -$( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#edit_request" ).submit(); - } - }); -}); -</script> - <br/><br/><ul class="manage-table-actions"> --- a/templates/webapps/galaxy/user/info.mako +++ b/templates/webapps/galaxy/user/info.mako @@ -2,31 +2,6 @@ <%namespace file="/user/info.mako" import="render_user_info" /><%namespace file="/message.mako" import="render_msg" /> -<script type="text/javascript"> -$( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#user_info" ).submit(); - } - }); -}); -</script> - %if message: ${render_msg( message, status )} %endif --- a/templates/admin/forms/edit_form.mako +++ b/templates/admin/forms/edit_form.mako @@ -6,31 +6,6 @@ %endif <script type="text/javascript"> -$( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#edit_form" ).submit(); - } - }); -}); -</script> - -<script type="text/javascript"> $(document).ready(function(){ //hide the all of the element with class msg_body $(".msg_body").hide(); --- a/templates/library/common/upload.mako +++ b/templates/library/common/upload.mako @@ -14,31 +14,6 @@ <%def name="javascripts()"> ${parent.javascripts()} ${h.js("jquery.autocomplete", "autocomplete_tagging" )} - - <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#upload_library_dataset" ).submit(); - } - }); - }); - </script></%def><%def name="stylesheets()"> --- a/templates/library/common/ldda_edit_info.mako +++ b/templates/library/common/ldda_edit_info.mako @@ -6,30 +6,6 @@ <%def name="javascripts()"> ${parent.javascripts()} ${h.js("jquery.autocomplete", "autocomplete_tagging" )} - <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#edit_info" ).submit(); - } - }); - }); - </script></%def><%def name="stylesheets()"> --- a/templates/library/common/library_dataset_info.mako +++ b/templates/library/common/library_dataset_info.mako @@ -4,30 +4,6 @@ <%def name="javascripts()"> ${parent.javascripts()} - <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#edit_info" ).submit(); - } - }); - }); - </script></%def> %if library_dataset == library_dataset.library_dataset_dataset_association.library_dataset: --- a/templates/requests/common/show_request.mako +++ b/templates/requests/common/show_request.mako @@ -19,29 +19,6 @@ <%def name="javascripts()"> ${parent.javascripts()} <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#show_request" ).submit(); - } - }); - }); - function showContent(vThis) { // http://www.javascriptjunkie.com --- a/templates/library/common/select_template.mako +++ b/templates/library/common/select_template.mako @@ -5,30 +5,6 @@ from galaxy.web.form_builder import CheckboxField inheritable_check_box = CheckboxField( 'inheritable' ) %> -<script type="text/javascript"> -$( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#select_template" ).submit(); - } - }); -}); -</script><br/><br/><ul class="manage-table-actions"> --- a/templates/library/common/ldda_info.mako +++ b/templates/library/common/ldda_info.mako @@ -25,30 +25,6 @@ <%def name="javascripts()"> ${parent.javascripts()} - <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#edit_info" ).submit(); - } - }); - }); - </script></%def> %if current_version:

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galaxy-dist commit 4990d7b95b72: Bug fix for signature of lib.galaxy_utils.sequence.transform.?NA_reverse_complement method.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg <dan(a)bx.psu.edu> # Date 1285944317 14400 # Node ID 4990d7b95b7273ba7159bfb2db1931a4e74a980a # Parent 7b431b0dbc687c1496ef5fba92dd443476d61d60 Bug fix for signature of lib.galaxy_utils.sequence.transform.?NA_reverse_complement method. --- a/lib/galaxy_utils/sequence/transform.py +++ b/lib/galaxy_utils/sequence/transform.py @@ -19,10 +19,10 @@ def DNA_complement( sequence ): def RNA_complement( sequence ): return sequence.translate( RNA_COMPLEMENT ) #returns the reverse complement of the sequence -def DNA_reverse_complement( self, sequence ): +def DNA_reverse_complement( sequence ): sequence = reverse( sequence ) return DNA_complement( sequence ) -def RNA_reverse_complement( self, sequence ): +def RNA_reverse_complement( sequence ): sequence = reverse( sequence ) return RNA_complement( sequence ) def to_DNA( sequence ):

1 0

galaxy-dist commit 8f2e21b07986: Enable export history jobs to work when application option 'outputs_to_working_directory' is set to true. This will enable export history jobs to work on galaxy main and, more generally, when galaxy datasets are mounted read-only.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1286208862 14400 # Node ID 8f2e21b079864cb02b2c4e5bfc3343cbf867e259 # Parent 06d6ce09e0f152d38c632dae7ccba9337f25bab5 Enable export history jobs to work when application option 'outputs_to_working_directory' is set to true. This will enable export history jobs to work on galaxy main and, more generally, when galaxy datasets are mounted read-only. --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -321,6 +321,20 @@ class JobWrapper( object ): inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] ) + + # Set up output dataset association for export history jobs. Because job + # uses a Dataset rather than an HDA or LDA, it's necessary to set up a + # fake dataset association that provides the needed attributes for + # preparing a job. + class FakeDatasetAssociation ( object ): + def __init__( self, dataset=None ): + self.dataset = dataset + self.file_name = dataset.file_name + self.metadata = dict() + self.children = [] + jeha = self.sa_session.query( model.JobExportHistoryArchive ).filter_by( job=job ).first() + if jeha: + out_data[ "output_file" ] = FakeDatasetAssociation( dataset=jeha.dataset ) # These can be passed on the command line if wanted as $userId $userEmail if job.history and job.history.user: # check for anonymous user! userId = '%d' % job.history.user.id @@ -632,13 +646,21 @@ class JobWrapper( object ): return self.false_path job = self.sa_session.query( model.Job ).get( self.job_id ) + # Job output datasets are combination of output datasets, library datasets, and jeha datasets. + jeha = self.sa_session.query( model.JobExportHistoryArchive ).filter_by( job=job ).first() if self.app.config.outputs_to_working_directory: self.output_paths = [] for name, data in [ ( da.name, da.dataset.dataset ) for da in job.output_datasets + job.output_library_datasets ]: false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % data.id ) ) self.output_paths.append( DatasetPath( data.id, data.file_name, false_path ) ) + if jeha: + false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % jeha.dataset.id ) ) + self.output_paths.append( DatasetPath( jeha.dataset.id, jeha.dataset.file_name, false_path ) ) else: self.output_paths = [ DatasetPath( da.dataset.dataset.id, da.dataset.file_name ) for da in job.output_datasets + job.output_library_datasets ] + if jeha: + self.output_paths.append( DatasetPath( jeha.dataset.id, jeha.dataset.file_name ) ) + return self.output_paths def get_output_file_id( self, file ): --- a/lib/galaxy/tools/imp_exp/__init__.py +++ b/lib/galaxy/tools/imp_exp/__init__.py @@ -15,12 +15,15 @@ def load_history_imp_exp_tools( toolbox <tool id="__EXPORT_HISTORY__" name="Export History" version="0.1" tool_type="export_history"><type class="ExportHistoryTool" module="galaxy.tools"/><action module="galaxy.tools.actions.history_imp_exp" class="ExportHistoryToolAction"/> - <command>$__SET_EXPORT_HISTORY_COMMAND_LINE__</command> + <command>$__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__ $output_file</command><inputs><param name="__HISTORY_TO_EXPORT__" type="hidden"/><param name="compress" type="boolean"/> - <param name="__SET_EXPORT_HISTORY_COMMAND_LINE__" type="hidden"/> + <param name="__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__" type="hidden"/></inputs> + <outputs> + <data format="gzip" name="output_file"/> + </outputs></tool> """ tmp_name = tempfile.NamedTemporaryFile() @@ -40,7 +43,9 @@ class JobExportHistoryArchiveWrapper( ob # jeha = job_export_history_archive for the job. """ Perform setup for job to export a history into an archive. Method generates attribute files for export, sets the corresponding attributes in the jeha - object, and returns a command line for running the job. """ + object, and returns a command line for running the job. The command line + includes the command, inputs, and options; it does not include the output + file because it must be set at runtime. """ # # Helper methods/classes. @@ -199,10 +204,9 @@ class JobExportHistoryArchiveWrapper( ob options = "" if jeha.compressed: options = "-G" - return "python %s %s %s %s %s %s" % ( + return "python %s %s %s %s %s" % ( os.path.join( os.path.abspath( os.getcwd() ), "lib/galaxy/tools/imp_exp/export_history.py" ), \ - options, history_attrs_filename, datasets_attrs_filename, jobs_attrs_filename, \ - jeha.dataset.file_name ) + options, history_attrs_filename, datasets_attrs_filename, jobs_attrs_filename ) def cleanup_after_job( self, db_session ): """ Remove temporary directory and attribute files generated during setup for this job. """ --- a/lib/galaxy/tools/actions/history_imp_exp.py +++ b/lib/galaxy/tools/actions/history_imp_exp.py @@ -61,7 +61,7 @@ class ExportHistoryToolAction( ToolActio # Set additional parameters. incoming[ '__HISTORY_TO_EXPORT__' ] = history.id - incoming[ '__SET_EXPORT_HISTORY_COMMAND_LINE__' ] = cmd_line + incoming[ '__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__' ] = cmd_line for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): job.add_parameter( name, value )

1 0

galaxy-dist commit 06d6ce09e0f1: Fix for checking whether the current user can access a specified library item.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1286207081 14400 # Node ID 06d6ce09e0f152d38c632dae7ccba9337f25bab5 # Parent 8774252ac0531343953428a44a5a2b07e6fe514e Fix for checking whether the current user can access a specified library item. --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -2246,22 +2246,30 @@ class LibraryCommon( BaseController, Use message=message, status=status ) ) def _check_access( self, trans, cntrller, is_admin, item, current_user_roles, use_panels, library_id, show_deleted ): + can_access = True if isinstance( item, trans.model.HistoryDatasetAssociation ): - # Deny that the dataset exists if the user does not have the DATASET_ACCESS permission. - if not item or \ - not ( trans.app.security_agent.can_access_dataset( current_user_roles, item.dataset ) and item.history.user==trans.user ): - message = "Invalid history dataset id (%s) specified." % str( item.id ) - return trans.response.send_redirect( web.url_for( controller='library_common', - action='browse_library', - cntrller=cntrller, - id=library_id, - show_deleted=show_deleted, - message=util.sanitize_text( message ), - status='error' ) ) - # Deny that the item exists if the user does not have the LIBRARY_ACCESS permission on its parent library, - # or if they are not able to access the item itself. - if not item or ( not is_admin and not trans.app.security_agent.can_access_library_item( current_user_roles, item, trans.user ) ): - message = "Invalid item id (%s) specified." % str( item.id ) + # Make sure the user has the DATASET_ACCESS permission on the history_dataset_association. + if not item: + message = "Invalid history dataset (%s) specified." % str( item ) + can_access = False + elif not trans.app.security_agent.can_access_dataset( current_user_roles, item.dataset ) and item.history.user==trans.user: + message = "You do not have permission to access the history dataset with id (%s)." % str( item.id ) + can_access = False + else: + # Make sure the user has the LIBRARY_ACCESS permission on the library item. + if not item: + message = "Invalid library item (%s) specified." % str( item ) + can_access = False + elif not ( is_admin or trans.app.security_agent.can_access_library_item( current_user_roles, item, trans.user ) ): + if isinstance( item, trans.model.Library ): + item_type = 'data library' + elif isinstance( item, trans.model.LibraryFolder ): + item_type = 'folder' + else: + item_type = '(unknown item type)' + message = "You do not have permission to access the %s with id (%s)." % ( item_type, str( item.id ) ) + can_access = False + if not can_access: if cntrller == 'api': return 400, message if isinstance( item, trans.model.Library ): @@ -2282,7 +2290,7 @@ class LibraryCommon( BaseController, Use def _check_add( self, trans, cntrller, is_admin, item, current_user_roles, use_panels, library_id, show_deleted ): # Deny access if the user is not an admin and does not have the LIBRARY_ADD permission. if not ( is_admin or trans.app.security_agent.can_add_library_item( current_user_roles, item ) ): - message = "You are not authorized to add an item to '%s'." % item.name + message = "You are not authorized to add an item to (%s)." % item.name # Redirect to the real parent library since we know we have access to it. if cntrller == 'api': return 403, message @@ -2300,7 +2308,7 @@ class LibraryCommon( BaseController, Use if not ( is_admin or \ ( trans.app.security_agent.can_manage_library_item( current_user_roles, item ) and trans.app.security_agent.can_manage_dataset( current_user_roles, library_dataset.library_dataset_dataset_association.dataset ) ) ): - message = "You are not authorized to manage permissions on library dataset '%s'." % library_dataset.name + message = "You are not authorized to manage permissions on library dataset (%s)." % library_dataset.name if cntrller == 'api': return 403, message return trans.response.send_redirect( web.url_for( controller='library_common', @@ -2312,7 +2320,7 @@ class LibraryCommon( BaseController, Use status='error' ) ) # Deny access if the user is not an admin and does not have the LIBRARY_MANAGE permission. if not ( is_admin or trans.app.security_agent.can_manage_library_item( current_user_roles, item ) ): - message = "You are not authorized to manage permissions on '%s'." % item.name + message = "You are not authorized to manage permissions on (%s)." % item.name if cntrller == 'api': return 403, message return trans.response.send_redirect( web.url_for( controller='library_common', @@ -2325,7 +2333,7 @@ class LibraryCommon( BaseController, Use def _check_modify( self, trans, cntrller, is_admin, item, current_user_roles, use_panels, library_id, show_deleted ): # Deny modification if the user is not an admin and does not have the LIBRARY_MODIFY permission. if not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, item ) ): - message = "You are not authorized to modify '%s'." % item.name + message = "You are not authorized to modify (%s)." % item.name if cntrller == 'api': return 403, message return trans.response.send_redirect( web.url_for( controller='library_common',

1 0

galaxy-dist commit 51aaa9eac818: Updates to LPS tool help text.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Richard Burhans <burhans(a)bx.psu.edu> # Date 1285871526 14400 # Node ID 51aaa9eac8182b25dbbffd1de902b78c916cb0f5 # Parent ddf70ed04c8b24f9095d4b16f6041907f7c6d428 Updates to LPS tool help text. --- a/tools/human_genome_variation/lps.xml +++ b/tools/human_genome_variation/lps.xml @@ -120,7 +120,7 @@ <param name="c1" type="float" value="1e-3" help="Parameter defining the margin by which the first-order step is required to decrease before being taken."><validator type="in_range" message="0.0 < c1 < 1.0" min="0.0" max="1.0"/></param> - <param name="maxIter" type="integer" value="10000" label="Maximum number of iterations"/> + <param name="maxIter" type="integer" value="10000" label="Maximum number of iterations" help="Terminate with error if we exceed this."/><param name="stopTol" type="float" value="1e-6" label="Stop tolerance" help="Convergence tolerance for target value of lambda."/><param name="intermediateTol" type="float" value="1e-4" label="Intermediate tolerance" help="Convergence tolerance for intermediate values of lambda."/><param name="finalOnly" type="select" format="integer" label="Final only"> @@ -132,8 +132,8 @@ </inputs><outputs> - <data name="output_file" format="tabular"/> - <data name="log_file" format="txt"/> + <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: results"/> + <data name="log_file" format="txt" label="${tool.name} on ${on_string}: log"/></outputs><requirements> @@ -188,28 +188,52 @@ There is a second output dataset (a log) **What it does** -The LASSO-Patternsearch algorithm efficiently identifies patterns of multiple -dichotomous risk factors for outcomes of interest in demographic and genomic -studies. It is designed for the case where there is a possibly very large -number of candidate patterns but it is believed that only a relatively small -number are important. +The LASSO-Patternsearch algorithm fits your dataset to an L1-regularized +logistic regression model. A benefit of using L1-regularization is +that it typically yields a weight vector with relatively few non-zero +coefficients. -If the "risky" direction (with respect to the outcome of interest) is known -for all or almost all variables, the results are readily interpretable. -If the risky direction is coded correctly for all of the variables, the -fitted model can be expected to be sparser than that for any other coding. -However, if a small number of risky variables are coded in the "wrong" way, -this usually can be detected. +For example, say you have a dataset containing M rows (subjects) +and N columns (attributes) where one of these N attributes is binary, +indicating whether or not the subject has some property of interest P. +In simple terms, LPS calculates a weight for each of the other attributes +in your dataset. This weight indicates how "relevant" that attribute +is for predicting whether or not a given subject has property P. +The L1-regularization causes most of these weights to be equal to zero, +which means LPS will find a "small" subset of the remaining N-1 attributes +in your dataset that can be used to predict P. -The input file is tabular with rows representing individuals and columns -representing variables. There is one special column, the label column, -containing +1 for cases, and -1 for controls. The other columns should be -0 or 1, with 1 representing the expected riskier value for each variable. -For instance with SNPs the column would have a 1 if the individual (row) -has the risk allele, or a 0 otherwise. The output file has one line for each -variable, or "feature" in the input file, with a single column containing the -calculated score for that feature. The log file provides information about -the input and the internal values obtained during the computation process. +In other words, LPS can be used for feature selection. + +The input dataset is tabular, and must contain a label column which +indicates whether or not a given row has property P. In the current +version of this tool, P must be encoded using +1 and -1. The Lambda_fac +parameter ranges from 0 to 1, and controls how sparse the weight +vector will be. At the low end, when Lambda_fac = 0, there will be +no regularization. At the high end, when Lambda_fac = 1, there will be +"too much" regularization, and all of the weights will equal zero. + +The LPS tool creates two output datasets. The first, called the results +file, is a tabular dataset containing one column of weights for each +value of the regularization parameter lambda that was tried. The weight +columns are in order from left to right by decreasing values of lambda. +The first N-1 rows in each column are the weights for the N-1 attributes +in your input dataset. The final row is a constant, the intercept. + +Let **x** be a row from your input dataset and let **b** be a column +from the results file. To compute the probability that row **x** has +a label value of +1: + + Probability(row **x** has label value = +1) = 1 / [1 + exp{**x** \* **b**\[1..n-1\] + **b**\[n\]}] + +where **x** \* **b**\[1..n-1\] represents matrix multiplication. + +The second output dataset, called the log file, is a text file which +contains additional data about the fitted L1-regularized logistic +regression model. These data include the number of features, the +computed value of lambda_max, the actual values of lambda used, the +optimal values of the log-likelihood and regularized log-likelihood +functions, the number of non-zeros, and the number of iterations. Website: http://pages.cs.wisc.edu/~swright/LPS/ @@ -235,11 +259,16 @@ Website: http://pages.cs.wisc.edu/~swrig - output log file:: - Data set has 100 vectors with 50 features - calculateLambdaMax: n=50, m=100, m+=50, m-=50 - computed value of lambda_max: 5.0000e-01 - lambda=2.50e-02 solution has 10 nonzeros. - It required 546 iterations + Data set has 100 vectors with 50 features. + calculateLambdaMax: n=50, m=100, m+=50, m-=50 + computed value of lambda_max: 5.0000e-01 + + lambda=2.96e-02 solution: + optimal log-likelihood function value: 6.46e-01 + optimal *regularized* log-likelihood function value: 6.79e-01 + number of nonzeros at the optimum: 5 + number of iterations required: 43 + etc. ----- --- a/test-data/lps_arrhythmia_log.txt +++ b/test-data/lps_arrhythmia_log.txt @@ -1,5 +1,4 @@ -Data set has 452 vectors with 279 features - +Data set has 452 vectors with 279 features. Sampled 452 points out of 452 calculateLambdaMax: n=279, m=452, m+=245, m-=207 computed value of lambda_max: 1.8231e+02 @@ -52,36 +51,147 @@ iter 1, gpnorm=1.7618e-09, nonzero= **** Initial point: nz=1, f= 0.689609056404, lambda= 5.469e+00 iter 1, gpnorm=1.7618e-09, nonzero= 1 ( 0.4%), function=6.896090564044e-01, alpha=3.2768e-01 Function evals = 2, Gradient evals = 1.0 -lambda=1.64e+02 solution has 1 nonzeros. -It required 6 iterations -lambda=1.17e+02 solution has 1 nonzeros. -It required 1 iterations +lambda=1.64e+02 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 6 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. -lambda=8.31e+01 solution has 1 nonzeros. -It required 1 iterations +lambda=1.17e+02 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. -lambda=5.91e+01 solution has 1 nonzeros. -It required 1 iterations +lambda=8.31e+01 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. -lambda=4.21e+01 solution has 1 nonzeros. -It required 1 iterations +lambda=5.91e+01 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. -lambda=3.00e+01 solution has 1 nonzeros. -It required 1 iterations +lambda=4.21e+01 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. -lambda=2.13e+01 solution has 1 nonzeros. -It required 1 iterations +lambda=3.00e+01 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. -lambda=1.52e+01 solution has 1 nonzeros. -It required 1 iterations +lambda=2.13e+01 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. -lambda=1.08e+01 solution has 1 nonzeros. -It required 1 iterations +lambda=1.52e+01 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. -lambda=7.68e+00 solution has 1 nonzeros. -It required 1 iterations +lambda=1.08e+01 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. -lambda=5.47e+00 solution has 1 nonzeros. -It required 1 iterations +lambda=7.68e+00 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. +lambda=5.47e+00 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. +

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galaxy-dist commit 8774252ac053: sample_tracking: migration script to modify the 'file_path' field type in 'sample_dataset' table to 'TEXT' so that it can support large file paths exceeding 255 characters
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1286199759 14400 # Node ID 8774252ac0531343953428a44a5a2b07e6fe514e # Parent e32d77e1f47b1fc94b3e7511094e4b0d760f1e97 sample_tracking: migration script to modify the 'file_path' field type in 'sample_dataset' table to 'TEXT' so that it can support large file paths exceeding 255 characters --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py @@ -0,0 +1,59 @@ +""" +Migration script to modify the 'file_path' field type in 'sample_dataset' table +to 'TEXT' so that it can support large file paths exceeding 255 characters +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +from sqlalchemy.exc import * + +from galaxy.model.custom_types import * +from galaxy.util.json import from_json_string, to_json_string + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + + +def upgrade(): + print __doc__ + metadata.reflect() + try: + SampleDataset_table = Table( "sample_dataset", metadata, autoload=True ) + except NoSuchTableError, e: + SampleDataset_table = None + log.debug( "Failed loading table 'sample_dataset'" ) + + if SampleDataset_table: + cmd = "SELECT id, file_path FROM sample_dataset" + result = db_session.execute( cmd ) + filepath_dict = {} + for r in result: + id = int(r[0]) + filepath_dict[id] = r[1] + # remove the 'file_path' column + try: + SampleDataset_table.c.file_path.drop() + except Exception, e: + log.debug( "Deleting column 'file_path' from the 'sample_dataset' table failed: %s" % ( str( e ) ) ) + # create the column again + try: + col = Column( "file_path", TEXT ) + col.create( SampleDataset_table ) + assert col is SampleDataset_table.c.file_path + except Exception, e: + log.debug( "Creating column 'file_path' in the 'sample_dataset' table failed: %s" % ( str( e ) ) ) + + for id, file_path in filepath_dict.items(): + cmd = "update sample_dataset set file_path='%s' where id=%i" % (file_path, id) + db_session.execute( cmd ) + +def downgrade(): + pass --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -620,7 +620,7 @@ SampleDataset.table = Table('sample_data Column( "update_time", DateTime, default=now, onupdate=now ), Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True ), Column( "name", TrimmedString( 255 ), nullable=False ), - Column( "file_path", TrimmedString( 255 ), nullable=False ), + Column( "file_path", TEXT ), Column( "status", TrimmedString( 255 ), nullable=False ), Column( "error_msg", TEXT ), Column( "size", TrimmedString( 255 ) ) )

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