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galaxy-dist commit ecc1cefbccba: Enhance GFFReader to read and return complete features (genes/transcripts), which are composed of multiple intervals/blocks. This required hacking around a couple limitations of bx-python, but these can be easily fixed when bx-python is updated. Use enhanced functionality to correctly create converted datasets for visualizing GFF files.
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 1289591537 18000 # Node ID ecc1cefbccba6135f824f9573f06c130fd6d08b4 # Parent b124f54952dee106f4ca87ea89a7f828c41562c3 Enhance GFFReader to read and return complete features (genes/transcripts), which are composed of multiple intervals/blocks. This required hacking around a couple limitations of bx-python, but these can be easily fixed when bx-python is updated. Use enhanced functionality to correctly create converted datasets for visualizing GFF files. Also updated GOPS tools to use a simpler GFF reader wrapper to read in intervals and convert to BED coordinates. --- a/tools/new_operations/gops_subtract.py +++ b/tools/new_operations/gops_subtract.py @@ -44,11 +44,11 @@ def main(): # Set readers to handle either GFF or default format. if in1_gff_format: - in1_reader_wrapper = GFFReaderWrapper + in1_reader_wrapper = GFFIntervalToBEDReaderWrapper else: in1_reader_wrapper = NiceReaderWrapper if in2_gff_format: - in2_reader_wrapper = GFFReaderWrapper + in2_reader_wrapper = GFFIntervalToBEDReaderWrapper else: in2_reader_wrapper = NiceReaderWrapper --- a/tools/new_operations/gops_intersect.py +++ b/tools/new_operations/gops_intersect.py @@ -44,11 +44,11 @@ def main(): # Set readers to handle either GFF or default format. if in1_gff_format: - in1_reader_wrapper = GFFReaderWrapper + in1_reader_wrapper = GFFIntervalToBEDReaderWrapper else: in1_reader_wrapper = NiceReaderWrapper if in2_gff_format: - in2_reader_wrapper = GFFReaderWrapper + in2_reader_wrapper = GFFIntervalToBEDReaderWrapper else: in2_reader_wrapper = NiceReaderWrapper @@ -66,10 +66,10 @@ def main(): fix_strand=True ) out_file = open( out_fname, "w" ) - + try: for line in intersect( [g1,g2], pieces=pieces, mincols=mincols ): - if type( line ) == GenomicInterval: + if isinstance( line, GenomicInterval ): if in1_gff_format: line = convert_bed_coords_to_gff( line ) out_file.write( "%s\n" % "\t".join( line.fields ) ) --- /dev/null +++ b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py @@ -0,0 +1,55 @@ +#!/usr/bin/env python + +""" +Convert from GFF file to interval index file. + +usage: + python gff_to_interval_index_converter.py [input] [output] +""" + +from __future__ import division + +import sys, fileinput +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +from galaxy.tools.util.gff_util import * +from bx.interval_index_file import Indexes + +def main(): + # Arguments + input_fname, out_fname = sys.argv[1:] + + # Do conversion. + chr_col, start_col, end_col, strand_col = ( 0, 3, 4, 6 ) + index = Indexes() + offset = 0 + reader_wrapper = GFFReaderWrapper( fileinput.FileInput( input_fname ), + chrom_col=chr_col, + start_col=start_col, + end_col=end_col, + strand_col=strand_col, + fix_strand=True ) + for feature in list( reader_wrapper ): + # TODO: need to address comments: + # if comment: + # increment_offset. + + # Add feature; index expects BED coordinates. + convert_gff_coords_to_bed( feature ) + index.add( feature.chrom, feature.start, feature.end, offset ) + + # Increment offset by feature length; feature length is all + # intervals/lines that comprise feature. + feature_len = 0 + for interval in feature.intervals: + # HACK: +1 for EOL char. Need bx-python to provide raw_line itself + # b/c TableReader strips EOL characters, thus changing the line + # length. + feature_len += len( interval.raw_line ) + 1 + offset += feature_len + + index.write( open(out_fname, "w") ) + +if __name__ == "__main__": + main() + --- a/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py +++ b/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py @@ -14,7 +14,7 @@ import pkg_resources; pkg_resources.requ from galaxy.visualization.tracks.summary import * from bx.intervals.io import * from bx.cookbook import doc_optparse -from galaxy.tools.util.gff_util import GFFReaderWrapper +from galaxy.tools.util.gff_util import * def main(): # Read options, args. @@ -40,9 +40,12 @@ def main(): strand_col=strand_col, fix_strand=True ) st = SummaryTree(block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30) - for line in list( reader_wrapper ): - if type( line ) is GenomicInterval: - st.insert_range( line.chrom, long( line.start ), long( line.end ) ) + for feature in list( reader_wrapper ): + if isinstance( feature, GenomicInterval ): + # Tree expects BED coordinates. + if type( feature ) is GFFFeature: + convert_gff_coords_to_bed( feature ) + st.insert_range( feature.chrom, long( feature.start ), long( feature.end ) ) st.write(out_fname) --- a/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml +++ b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml @@ -1,6 +1,6 @@ -<tool id="CONVERTER_gff_to_interval_index_0" name="Convert BED to Interval Index" version="1.0.0" hidden="true"> +<tool id="CONVERTER_gff_to_interval_index_0" name="Convert GFF to Interval Index" version="1.0.0" hidden="true"> - <command interpreter="python">interval_to_interval_index_converter.py $input1 $output1 --gff</command> + <command interpreter="python">gff_to_interval_index_converter.py $input1 $output1</command><inputs><page><param format="gff" name="input1" type="data" label="Choose GFF file"/> --- a/tools/new_operations/flanking_features.py +++ b/tools/new_operations/flanking_features.py @@ -153,11 +153,11 @@ def main(): # Set readers to handle either GFF or default format. if in1_gff_format: - in1_reader_wrapper = GFFReaderWrapper + in1_reader_wrapper = GFFIntervalToBEDReaderWrapper else: in1_reader_wrapper = NiceReaderWrapper if in2_gff_format: - in2_reader_wrapper = GFFReaderWrapper + in2_reader_wrapper = GFFIntervalToBEDReaderWrapper else: in2_reader_wrapper = NiceReaderWrapper --- a/lib/galaxy/tools/util/gff_util.py +++ b/lib/galaxy/tools/util/gff_util.py @@ -2,25 +2,173 @@ Provides utilities for working with GFF files. """ -from bx.intervals.io import NiceReaderWrapper, GenomicInterval +from bx.intervals.io import * + +class GFFInterval( GenomicInterval ): + """ + A GFF interval, including attributes. If file is strictly a GFF file, + only attribute is 'group.' + """ + def __init__( self, reader, fields, chrom_col, start_col, end_col, strand_col, default_strand, \ + fix_strand=False, raw_line='' ): + GenomicInterval.__init__( self, reader, fields, chrom_col, start_col, end_col, strand_col, \ + default_strand, fix_strand=fix_strand ) + self.raw_line = raw_line + self.attributes = parse_gff_attributes( fields[8] ) + +class GFFFeature( GenomicInterval ): + """ + A GFF feature, which can include multiple intervals. + """ + def __init__( self, reader, chrom_col, start_col, end_col, strand_col, default_strand, \ + fix_strand=False, intervals=[] ): + GenomicInterval.__init__( self, reader, intervals[0].fields, chrom_col, start_col, end_col, \ + strand_col, default_strand, fix_strand=fix_strand ) + self.intervals = intervals + # Use intervals to set feature attributes. + for interval in self.intervals: + # Error checking. + if interval.chrom != self.chrom: + raise ValueError( "interval chrom does not match self chrom: %i != %i" % \ + ( interval.chrom, self.chrom ) ) + if interval.strand != self.strand: + raise ValueError( "interval strand does not match self strand: %s != %s" % \ + ( interval.strand, self.strand ) ) + # Set start, end of interval. + if interval.start < self.start: + self.start = interval.start + if interval.end > self.end: + self.end = interval.end + +class GFFIntervalToBEDReaderWrapper( NiceReaderWrapper ): + """ + Reader wrapper that reads GFF intervals/lines and automatically converts + them to BED format. + """ + + def parse_row( self, line ): + # HACK: this should return a GFF interval, but bx-python operations + # require GenomicInterval objects and subclasses will not work. + interval = GenomicInterval( self, line.split( "\t" ), self.chrom_col, self.start_col, \ + self.end_col, self.strand_col, self.default_strand, \ + fix_strand=self.fix_strand ) + interval = convert_gff_coords_to_bed( interval ) + return interval class GFFReaderWrapper( NiceReaderWrapper ): """ - Reader wrapper converts GFF format--starting and ending coordinates are 1-based, closed--to the - 'traditional'/BED interval format--0 based, half-open. This is useful when using GFF files as inputs - to tools that expect traditional interval format. + Reader wrapper for GFF files. + + Wrapper has two major functions: + (1) group entries for GFF file (via group column), GFF3 (via id attribute ), + or GTF (via gene_id/transcript id); + (2) convert coordinates from GFF format--starting and ending coordinates + are 1-based, closed--to the 'traditional'/BED interval format--0 based, + half-open. This is useful when using GFF files as inputs to tools that + expect traditional interval format. """ + + def __init__( self, reader, **kwargs ): + """ + Create wrapper. Defaults are group_entries=False and + convert_coords_to_bed=True to support backward compatibility. + """ + NiceReaderWrapper.__init__( self, reader, **kwargs ) + self.group_entries = kwargs.get( 'group_entries', False ) + self.convert_coords_to_bed = kwargs.get( 'convert_coords_to_bed', True ) + self.last_line = None + self.cur_offset = 0 + self.seed_interval = None + def parse_row( self, line ): - interval = GenomicInterval( self, line.split( "\t" ), self.chrom_col, self.start_col, self.end_col, \ - self.strand_col, self.default_strand, fix_strand=self.fix_strand ) - interval = convert_gff_coords_to_bed( interval ) + interval = GFFInterval( self, line.split( "\t" ), self.chrom_col, self.start_col, \ + self.end_col, self.strand_col, self.default_strand, \ + fix_strand=self.fix_strand, raw_line=line ) + if self.convert_coords_to_bed: + interval = convert_gff_coords_to_bed( interval ) return interval + def next( self ): + """ Returns next GFFFeature. """ + + # + # Helper function. + # + + def handle_parse_error( parse_error ): + """ Actions to take when ParseError found. """ + if self.outstream: + if self.print_delegate and hasattr(self.print_delegate,"__call__"): + self.print_delegate( self.outstream, e, self ) + self.skipped += 1 + # no reason to stuff an entire bad file into memmory + if self.skipped < 10: + self.skipped_lines.append( ( self.linenum, self.current_line, str( e ) ) ) + + # + # Get next GFFFeature + # + + # If there is no seed interval, set one. Also, if there are no more + # intervals to read, this is where iterator dies. + if not self.seed_interval: + while not self.seed_interval: + try: + self.seed_interval = GenomicIntervalReader.next( self ) + except ParseError, e: + handle_parse_error( e ) + + # Initialize feature name from seed. + feature_group = self.seed_interval.attributes.get( 'group', None ) # For GFF + feature_id = self.seed_interval.attributes.get( 'id', None ) # For GFF3 + feature_gene_id = self.seed_interval.attributes.get( 'gene_id', None ) # For GTF + feature_transcript_id = self.seed_interval.attributes.get( 'transcript_id', None ) # For GTF + + # Read all intervals associated with seed. + feature_intervals = [] + feature_intervals.append( self.seed_interval ) + while True: + try: + interval = GenomicIntervalReader.next( self ) + except StopIteration, e: + # No more intervals to read, but last feature needs to be + # returned. + interval = None + break + except ParseError, e: + handle_parse_error( e ) + + # If interval not associated with feature, break. + group = interval.attributes.get( 'group', None ) + if group and feature_group != group: + break + id = interval.attributes.get( 'id', None ) + if id and feature_id != id: + break + gene_id = interval.attributes.get( 'gene_id', None ) + transcript_id = interval.attributes.get( 'transcript_id', None ) + if transcript_id and transcript_id != feature_transcript_id and gene_id and \ + gene_id != feature_gene_id: + break + + # Interval associated with feature. + feature_intervals.append( interval ) + + # Last interval read is the seed for the next interval. + self.seed_interval = interval + + # Return GFF feature with all intervals. + return GFFFeature( self, self.chrom_col, self.start_col, self.end_col, self.strand_col, \ + self.default_strand, fix_strand=self.fix_strand, \ + intervals=feature_intervals ) + + def convert_bed_coords_to_gff( interval ): """ - Converts an interval object's coordinates from BED format to GFF format. Accepted object types include - GenomicInterval and list (where the first element in the list is the interval's start, and the second - element is the interval's end). + Converts an interval object's coordinates from BED format to GFF format. + Accepted object types include GenomicInterval and list (where the first + element in the list is the interval's start, and the second element is + the interval's end). """ if type( interval ) is GenomicInterval: interval.start += 1 @@ -30,9 +178,10 @@ def convert_bed_coords_to_gff( interval def convert_gff_coords_to_bed( interval ): """ - Converts an interval object's coordinates from GFF format to BED format. Accepted object types include - GenomicInterval and list (where the first element in the list is the interval's start, and the second - element is the interval's end). + Converts an interval object's coordinates from GFF format to BED format. + Accepted object types include GenomicInterval and list (where the first + element in the list is the interval's start, and the second element is + the interval's end). """ if type( interval ) is GenomicInterval: interval.start -= 1 @@ -42,10 +191,15 @@ def convert_gff_coords_to_bed( interval def parse_gff_attributes( attr_str ): """ - Parses a GFF/GTF attribute string and returns a dictionary of name-value pairs. - The general format for a GFF3 attributes string is name1=value1;name2=value2 - The general format for a GTF attribute string is name1 "value1" ; name2 "value2" - """ + Parses a GFF/GTF attribute string and returns a dictionary of name-value + pairs. The general format for a GFF3 attributes string is + name1=value1;name2=value2 + The general format for a GTF attribute string is + name1 "value1" ; name2 "value2" + The general format for a GFF attribute string is a single string that + denotes the interval's group; in this case, method returns a dictionary + with a single key-value pair, and key name is 'group' + """ attributes_list = attr_str.split(";") attributes = {} for name_value_pair in attributes_list: @@ -53,6 +207,9 @@ def parse_gff_attributes( attr_str ): pair = name_value_pair.strip().split(" ") if len( pair ) == 1: pair = name_value_pair.strip().split("=") + if len( pair ) == 1: + # Could not split for some reason -- raise exception? + continue if pair == '': continue name = pair[0].strip() @@ -61,4 +218,9 @@ def parse_gff_attributes( attr_str ): # Need to strip double quote from values value = pair[1].strip(" \"") attributes[ name ] = value + + if len( attributes ) == 0: + # Could not split attributes string, so entire string must be + # 'group' attribute. This is the case for strictly GFF files. + attributes['group'] = attr_str return attributes

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galaxy-dist commit b124f54952de: Small fixes and refactor to workflows: remove unused ensure_popup_helper(), and fix extra comma that was returning error in IE.
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 1289591135 18000 # Node ID b124f54952dee106f4ca87ea89a7f828c41562c3 # Parent b7f712cecaa9f527f1161f923ebe798eba526cb6 Small fixes and refactor to workflows: remove unused ensure_popup_helper(), and fix extra comma that was returning error in IE. --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -13,7 +13,6 @@ ensure_dd_helper(); make_left_panel( $("#left"), $("#center"), $("#left-border" ) ); make_right_panel( $("#right"), $("#center"), $("#right-border" ) ); - ensure_popup_helper(); ## handle_minwidth_hint = rp.handle_minwidth_hint; </script></%def> @@ -82,8 +81,7 @@ "${initial_text}": function() { // Show/hide menu and update vars, user preferences. var menu = $('#tool-search'); - if (menu.is(":visible")) - { + if (menu.is(":visible")) { // Hide menu. pref_value = "False"; menu_option_text = "Search Tools"; @@ -91,9 +89,7 @@ // Reset search. reset_tool_search(true); - } - else - { + } else { // Show menu. pref_value = "True"; menu_option_text = "Hide Search"; @@ -158,18 +154,17 @@ var next = this_label.next(); var no_visible_tools = true; // Look through tools following label and, if none are visible, hide label. - while (next.length != 0 && next.hasClass("toolTitle")) - { - if (next.is(":visible")) - { + while (next.length !== 0 && next.hasClass("toolTitle")) { + if (next.is(":visible")) { no_visible_tools = false; break; + } else { + next = next.next(); } - else - next = next.next(); } - if (no_visible_tools) + if (no_visible_tools) { this_label.hide(); + } }); } else { $("#search-no-results").show(); @@ -211,9 +206,9 @@ scroll_to_nodes(); canvas_manager.draw_overview(); // Determine if any parameters were 'upgraded' and provide message - upgrade_message = "" - $.each( data['upgrade_messages'], function( k, v ) { - upgrade_message += ( "<li>Step " + ( parseInt(k) + 1 ) + ": " + workflow.nodes[k].name + "<ul>"); + upgrade_message = ""; + $.each( data.upgrade_messages, function( k, v ) { + upgrade_message += ( "<li>Step " + ( parseInt(k, 10) + 1 ) + ": " + workflow.nodes[k].name + "<ul>"); $.each( v, function( i, vv ) { upgrade_message += "<li>" + vv +"</li>"; }); @@ -256,7 +251,7 @@ "Layout": layout_editor, "Save" : save_current_workflow, ##"Load a Workflow" : load_workflow, - "Close": close_editor, + "Close": close_editor }); function edit_workflow_outputs(){ @@ -297,21 +292,21 @@ workflow.has_changes = true; }); $('#workflow-output-area').show(); - }; + } function layout_editor() { workflow.layout(); workflow.fit_canvas_to_nodes(); scroll_to_nodes(); canvas_manager.draw_overview(); - }; + } function edit_workflow_attributes() { workflow.clear_active_node(); $('.right-content').hide(); $('#edit-attributes').show(); - }; + } $.jStore.engineReady(function() { // On load, set the size to the pref stored in local storage if it exists @@ -354,7 +349,11 @@ // Lets the overview be toggled visible and invisible, adjusting the arrows accordingly $("#close-viewport").click( function() { - $("#overview-border").css("right") == "0px" ? hide_overview() : show_overview(); + if ( $("#overview-border").css("right") === "0px" ) { + hide_overview(); + } else { + show_overview(); + } }); // Unload handler @@ -405,7 +404,7 @@ function scroll_to_nodes() { var cv = $("#canvas-viewport"); - var cc = $("#canvas-container") + var cc = $("#canvas-container"); var top, left; if ( cc.width() < cv.width() ) { left = ( cv.width() - cc.width() ) / 2; @@ -436,14 +435,14 @@ node.init_field_data( data ); }, error: function( x, e ) { - var m = "error loading field data" - if ( x.status == 0 ) { - m += ", server unavailable" + var m = "error loading field data"; + if ( x.status === 0 ) { + m += ", server unavailable"; } node.error( m ); } }); - }; + } function add_node_for_module( type, title ) { node = prebuild_node( type, title ); @@ -466,7 +465,7 @@ node.error( m ); } }); - }; + } <% from galaxy.jobs.actions.post import ActionBox @@ -500,12 +499,12 @@ } function new_pja(action_type, target, node){ - if (node.post_job_actions == undefined){ + if (node.post_job_actions === undefined){ //New tool node, set up dict. node.post_job_actions = {}; } - if (node.post_job_actions[action_type+target] == undefined){ - var new_pja = new Object(); + if (node.post_job_actions[action_type+target] === undefined){ + var new_pja = {}; new_pja.action_type = action_type; new_pja.output_name = target; node.post_job_actions[action_type+target] = null; @@ -513,7 +512,7 @@ display_pja(new_pja, node); workflow.active_form_has_changes = true; return true; - }else{ + } else { return false; } } @@ -576,7 +575,7 @@ var value = $(this).attr( 'value' ); options[ $(this).text() ] = function() { $(form).append( "<input type='hidden' name='"+name+"' value='"+value+"' />" ).submit(); - } + }; }); b.insertAfter( this ); $(this).remove(); @@ -613,9 +612,9 @@ "Don't Save": do_close } ); } else { - window.document.location = "${next_url}" + window.document.location = "${next_url}"; } - } + }; var save_current_workflow = function ( eventObj, success_callback ) { show_modal( "Saving workflow", "progress" ); @@ -634,14 +633,14 @@ type: "POST", data: { id: "${trans.security.encode_id( stored.id )}", - workflow_data: function() { return JSON.stringify( workflow.to_simple() ) }, + workflow_data: function() { return JSON.stringify( workflow.to_simple() ); }, "_": "true" }, dataType: 'json', success: function( data ) { var body = $("<div></div>").text( data.message ); if ( data.errors ) { - body.addClass( "warningmark" ) + body.addClass( "warningmark" ); var errlist = $( "<ul/>" ); $.each( data.errors, function( i, v ) { $("<li></li>").text( v ).appendTo( errlist ); @@ -663,7 +662,7 @@ } } }); - } + }; // We bind to ajaxStop because of auto-saving, since the form submission ajax // call needs to be completed so that the new data is saved @@ -677,7 +676,7 @@ } else { savefn(success_callback); } - } + }; </script></%def>

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galaxy-dist commit caed55b53f5a: Allows the downloading of metadata files associated with datasets (such as bai indices for bam files). This is done by adding a dropdown menu to the Save icon of appropriate datasets. Could potentially be modified to access implicitly converted datatypes as well in the future. Closes #410
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 1289525191 18000 # Node ID caed55b53f5a811226e0bfa1c177e7b3e57a909a # Parent ff7327f2946e9121139cefbf4a45dba2791b7162 Allows the downloading of metadata files associated with datasets (such as bai indices for bam files). This is done by adding a dropdown menu to the Save icon of appropriate datasets. Could potentially be modified to access implicitly converted datatypes as well in the future. Closes #410 --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -1,8 +1,10 @@ <% _=n_ %> ## Render the dataset `data` as history item, using `hid` as the displayed id <%def name="render_dataset( data, hid, show_deleted_on_refresh = False, for_editing = True )"> - <a name="${trans.security.encode_id( data.id )}"></a><% + dataset_id = trans.security.encode_id( data.id ) + from galaxy.datatypes.metadata import FileParameter + if data.state in ['no state','',None]: data_state = "queued" else: @@ -41,7 +43,6 @@ %endif %else: <% - dataset_id = trans.security.encode_id( data.id ) if for_editing: display_url = h.url_for( controller='dataset', action='display', dataset_id=dataset_id, preview=True, filename='' ) else: @@ -117,10 +118,25 @@ %endif </div><div class="info">${_('Info: ')}${data.display_info()}</div> - <div> - <% dataset_id=trans.security.encode_id( data.id ) %> + <div> %if data.has_data(): + + ## Check for downloadable metadata files + <% meta_files = [ k for k in data.metadata.spec.keys() if isinstance( data.metadata.spec[k].param, FileParameter ) ] %> + %if meta_files: + <div popupmenu="dataset-${dataset_id}-popup"> + %for file_type in meta_files: + <a class="action-button" href="${h.url_for( controller='dataset', action='get_metadata_file', hda_id=dataset_id, metadata_type=file_type )}"> + Download ${file_type}</a> + %endfor + </div> + <div style="float:left;" class="menubutton split popup" id="dataset-${dataset_id}-popup"> + %endif <a href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, to_ext=data.ext )}" title="Save" class="icon-button disk tooltip"></a> + %if meta_files: + </div> + %endif + %if for_editing: <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> %if app.config.get_bool( 'enable_tracks', False ) and data.ext in app.datatypes_registry.get_available_tracks(): --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -277,6 +277,7 @@ var updater_callback = function ( tracke // Keep going (if there are still any items to track) updater( tracked_datasets ); } + make_popup_menus(); }, error: function() { // Just retry, like the old method, should try to be smarter --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -305,7 +305,18 @@ class DatasetInterface( BaseController, return trans.show_error_message( msg ) - + @web.expose + def get_metadata_file(self, trans, hda_id, metadata_type): + """ Allows the downloading of metadata files associated with datasets (eg. bai index for bam files) """ + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( hda_id ) ) + if not data or not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ): + return trans.show_error_message( "You are not allowed to access this dataset" ) + + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = ''.join(c in valid_chars and c or '_' for c in data.name)[0:150] + trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy%s-[%s].%s" % (data.hid, fname, metadata_type) + return open(data.metadata.get(metadata_type).file_name) + @web.expose def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, **kwd): """Catches the dataset id and displays file contents as directed""" @@ -323,8 +334,7 @@ class DatasetInterface( BaseController, data = None if not data: raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) - current_user_roles = trans.get_current_user_roles() - if not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): + if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ): return trans.show_error_message( "You are not allowed to access this dataset" ) if data.state == trans.model.Dataset.states.UPLOAD: @@ -358,8 +368,7 @@ class DatasetInterface( BaseController, if not to_ext: to_ext = data.extension valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - fname = data.name - fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] + fname = ''.join(c in valid_chars and c or '_' for c in data.name)[0:150] trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy%s-[%s].%s" % (data.hid, fname, to_ext) return open( data.file_name ) if not os.path.exists( data.file_name ):

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galaxy-dist commit 122aaabe2c7e: Workaround Issue 397 using 'if' in Cheetah template to avoid hidden parameters
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 peterjc <p.j.a.cock(a)googlemail.com> # Date 1286965628 -3600 # Node ID 122aaabe2c7eb48726f65233370926b838b6b444 # Parent 10d0ffe5b7e22b2d122945ab5b7fa951a18c6e4a Workaround Issue 397 using 'if' in Cheetah template to avoid hidden parameters --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -12,11 +12,12 @@ blastn #end if -task $blast_type -evalue $evalue_cutoff -$adv_opts.filter_query -$adv_opts.strand -out $output1 $out_format -num_threads 8 +#if $adv_opts.adv_opts_selector=="advanced": +$adv_opts.filter_query +$adv_opts.strand ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): @@ -26,6 +27,8 @@ blastn -word_size $adv_opts.word_size #end if $adv_opts.ungapped +## End of advanced options: +#end if </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -78,13 +81,7 @@ blastn <option value="basic" selected="True">Hide Advanced Options</option><option value="advanced">Show Advanced Options</option></param> - <when value="basic"> - <param name="filter_query" type="hidden" value="" /> - <param name="strand" type="hidden" value="" /> - <param name="max_hits" type="hidden" value="" /> - <param name="word_size" type="hidden" value="" /> - <param name="ungapped" type="hidden" value="" /> - </when> + <when value="basic" /><when value="advanced"><param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -12,11 +12,12 @@ blastp #end if -task $blast_type -evalue $evalue_cutoff -$adv_opts.filter_query -$adv_opts.matrix -out $output1 $out_format -num_threads 8 +#if $adv_opts.adv_opts_selector=="advanced": +$adv_opts.filter_query +$adv_opts.matrix ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): @@ -27,6 +28,8 @@ blastp #end if ##Ungapped disabled for now - see comments below ##$adv_opts.ungapped +## End of advanced options: +#end if </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> @@ -73,16 +76,7 @@ blastp <option value="basic" selected="True">Hide Advanced Options</option><option value="advanced">Show Advanced Options</option></param> - <when value="basic"> - <param name="filter_query" type="hidden" value="" /> - <param name="matrix" type="hidden" value="" /> - <param name="max_hits" type="hidden" value="" /> - <param name="word_size" type="hidden" value="" /> -  - </when> + <when value="basic" /><when value="advanced"><param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -11,12 +11,13 @@ tblastx -subject "$db_opts.subject" #end if -evalue $evalue_cutoff +-out $output1 +$out_format +-num_threads 8 +#if $adv_opts.adv_opts_selector=="advanced": $adv_opts.filter_query $adv_opts.strand $adv_opts.matrix --out $output1 -$out_format --num_threads 8 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): @@ -25,6 +26,8 @@ tblastx #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): -word_size $adv_opts.word_size #end if +## End of advanced options: +#end if </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -67,13 +70,7 @@ tblastx <option value="basic" selected="True">Hide Advanced Options</option><option value="advanced">Show Advanced Options</option></param> - <when value="basic"> - <param name="filter_query" type="hidden" value="" /> - <param name="strand" type="hidden" value="" /> - <param name="matrix" type="hidden" value="" /> - <param name="max_hits" type="hidden" value="" /> - <param name="word_size" type="hidden" value="" /> - </when> + <when value="basic" /><when value="advanced"><param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -11,12 +11,13 @@ blastx -subject "$db_opts.subject" #end if -evalue $evalue_cutoff +-out $output1 +$out_format +-num_threads 8 +#if $adv_opts.adv_opts_selector=="advanced": $adv_opts.filter_query $adv_opts.strand $adv_opts.matrix --out $output1 -$out_format --num_threads 8 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): @@ -26,6 +27,8 @@ blastx -word_size $adv_opts.word_size #end if $adv_opts.ungapped +## End of advanced options: +#end if </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -68,14 +71,7 @@ blastx <option value="basic" selected="True">Hide Advanced Options</option><option value="advanced">Show Advanced Options</option></param> - <when value="basic"> - <param name="filter_query" type="hidden" value="" /> - <param name="strand" type="hidden" value="" /> - <param name="matrix" type="hidden" value="" /> - <param name="max_hits" type="hidden" value="" /> - <param name="word_size" type="hidden" value="" /> - <param name="ungapped" type="hidden" value="" /> - </when> + <when value="basic" /><when value="advanced"><param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -11,11 +11,12 @@ tblastn -subject "$db_opts.subject" #end if -evalue $evalue_cutoff -$adv_opts.filter_query -$adv_opts.matrix -out $output1 $out_format -num_threads 8 +#if $adv_opts.adv_opts_selector=="advanced": +$adv_opts.filter_query +$adv_opts.matrix ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): @@ -26,6 +27,8 @@ tblastn #end if ##Ungapped disabled for now - see comments below ##$adv_opts.ungapped +## End of advanced options: +#end if </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> @@ -68,16 +71,7 @@ tblastn <option value="basic" selected="True">Hide Advanced Options</option><option value="advanced">Show Advanced Options</option></param> - <when value="basic"> - <param name="filter_query" type="hidden" value="" /> - <param name="matrix" type="hidden" value="" /> - <param name="max_hits" type="hidden" value="" /> - <param name="word_size" type="hidden" value="" /> -  - </when> + <when value="basic" /><when value="advanced"><param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />

1 0

galaxy-dist commit dfc848840870: Various sample tracking bug fixes: samples no longer require bar codes, change all references to 'barcode' to be 'bar_code' since that is what the model uses, and mixing the 2 is not maintainable, enhance sample popup menu options, fix broken logic that handles bulk sample library and folderr changes.
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 1289503442 18000 # Node ID dfc848840870fa9936a69e62322446fcb940fb40 # Parent ca23ea683d26df004e666ede82950c712e3ac637 Various sample tracking bug fixes: samples no longer require bar codes, change all references to 'barcode' to be 'bar_code' since that is what the model uses, and mixing the 2 is not maintainable, enhance sample popup menu options, fix broken logic that handles bulk sample library and folderr changes. --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -725,7 +725,7 @@ class RequestsCommon( BaseController, Us search_type = params.get( 'search_type', '' ) request_states = util.listify( params.get( 'request_states', '' ) ) samples = [] - if search_type == 'barcode': + if search_type == 'bar_code': samples = trans.sa_session.query( trans.model.Sample ) \ .filter( and_( trans.model.Sample.table.c.deleted==False, func.lower( trans.model.Sample.table.c.bar_code ).like( "%" + search_string.lower() + "%" ) ) ) \ @@ -763,7 +763,7 @@ class RequestsCommon( BaseController, Us display='checkboxes' ) # Build the search_type SelectField selected_value = kwd.get( 'search_type', 'sample name' ) - types = [ 'sample name', 'barcode', 'dataset' ] + types = [ 'sample name', 'bar_code', 'dataset' ] search_type = build_select_field( trans, types, 'self', 'search_type', selected_value=selected_value, refresh_on_change=False ) # Build the search_box TextField search_box = TextField( 'search_box', 50, kwd.get('search_box', '' ) ) @@ -846,7 +846,7 @@ class RequestsCommon( BaseController, Us # Append the new sample to the current list of samples for the request displayable_sample_widgets.append( dict( id=None, name=name, - barcode='', + bar_code='', library=None, library_id=library_id, folder=None, @@ -999,7 +999,7 @@ class RequestsCommon( BaseController, Us **kwd ) displayable_sample_widgets.append( dict( id=None, name=row[0], - barcode='', + bar_code='', library=None, folder=None, library_select_field=library_select_field, @@ -1029,7 +1029,10 @@ class RequestsCommon( BaseController, Us editing_samples=False ) def __save_samples( self, trans, cntrller, request, samples, **kwd ): # Here we handle saving all new samples added by the user as well as saving - # changes to any subset of the request's samples. + # changes to any subset of the request's samples. A sample will not have an + # associated SampleState until the request is submitted, at which time the + # sample is automatically associated with the first SampleState configured by + # the admin for the request's RequestType. params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -1065,7 +1068,7 @@ class RequestsCommon( BaseController, Us # Send the encoded sample_ids to update_sample_state. # TODO: make changes necessary to just send the samples... encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) - # Make sure all samples have a unique barcode if the state is changing + # Make sure all samples have a unique bar_code if the state is changing for sample_index in range( len( samples ) ): current_sample = samples[ sample_index ] if current_sample is None: @@ -1073,13 +1076,15 @@ class RequestsCommon( BaseController, Us # on which to perform the action. continue request_sample = request.samples[ sample_index ] - bc_message = self.__validate_barcode( trans, request_sample, current_sample[ 'barcode' ] ) - if bc_message: - #status = 'error' - message += bc_message - kwd[ 'message' ] = message - del kwd[ 'save_samples_button' ] - handle_error( **kwd ) + bar_code = current_sample[ 'bar_code' ] + if bar_code: + # If the sample has a new bar_code, make sure it is unique. + bc_message = self.__validate_bar_code( trans, request_sample, bar_code ) + if bc_message: + message += bc_message + kwd[ 'message' ] = message + del kwd[ 'save_samples_button' ] + handle_error( **kwd ) self.update_sample_state( trans, cntrller, encoded_selected_sample_ids, new_state, comment=sample_event_comment ) return trans.response.send_redirect( web.url_for( controller='requests_common', cntrller=cntrller, @@ -1088,18 +1093,22 @@ class RequestsCommon( BaseController, Us elif sample_operation == 'Select data library and folder': # TODO: fix the code so that the sample_operation_select_field does not use # sample_0_library_id as it's name. it should use something like sample_operation_library_id - # and sample_operation-folder_id because the name sample_0_library_id should belong to the + # and sample_operation_folder_id because the name sample_0_library_id should belong to the # first sample since all other form field values are named like this. The library and folder # are skewed to be named +1 resulting in the forced use of id_index everywhere... library_id = params.get( 'sample_0_library_id', 'none' ) folder_id = params.get( 'sample_0_folder_id', 'none' ) library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) + for sample_index in range( len( samples ) ): + current_sample = samples[ sample_index ] + current_sample[ 'library' ] = library + current_sample[ 'folder' ] = folder self.__update_samples( trans, cntrller, request, samples, **kwd ) # Samples will not have an associated SampleState until the request is submitted, at which # time all samples of the request will be set to the first SampleState configured for the # request's RequestType defined by the admin. if request.is_submitted: - # See if all the samples' barcodes are in the same state, and if so send email if configured to. + # See if all the samples' bar_codes are in the same state, and if so send email if configured to. common_state = request.samples_have_common_state if common_state and common_state.id == request.type.states[1].id: comment = "All samples of this request are in the (%s) sample state. " % common_state.name @@ -1136,10 +1145,12 @@ class RequestsCommon( BaseController, Us status=status, message=message ) ) def __update_samples( self, trans, cntrller, request, sample_widgets, **kwd ): - # Determine if the values in kwd require updating the request's samples. The list of - # sample_widgets must have the same number of objects as request.samples, but some of - # the objects can be None. Those that are not None correspond to samples selected by - # the user for performing an action on multiple samples simultaneously. + # The list of sample_widgets must have the same number of objects as request.samples, + # but some of the objects can be None. Those that are not None correspond to samples + # selected by the user for performing an action on multiple samples simultaneously. + # The items in the sample_widgets list have already been populated with any changed + # param values (changed implies the value in kwd is different from the attribute value + # in the database) in kwd before this method is reached. def handle_error( **kwd ): kwd[ 'status' ] = 'error' return trans.response.send_redirect( web.url_for( controller='requests_common', @@ -1147,12 +1158,6 @@ class RequestsCommon( BaseController, Us cntrller=cntrller, **kwd ) ) params = util.Params( kwd ) - sample_operation = params.get( 'sample_operation', 'none' ) - if sample_operation != 'none': - # These values will be in kwd if the user checked 1 or more checkboxes for performing this action - # on a set of samples. - library_id = params.get( 'sample_0_library_id', 'none' ) - folder_id = params.get( 'sample_0_folder_id', 'none' ) for index, sample_widget in enumerate( sample_widgets ): if sample_widget is not None: # sample_widget will be None if the user checked sample check boxes and selected an action @@ -1161,21 +1166,16 @@ class RequestsCommon( BaseController, Us # Get the sample's form values to see if they have changed. form_values = trans.sa_session.query( trans.model.FormValues ).get( sample.values.id ) if sample.name != sample_widget[ 'name' ] or \ - sample.bar_code != sample_widget[ 'barcode' ] or \ + sample.bar_code != sample_widget[ 'bar_code' ] or \ sample.library != sample_widget[ 'library' ] or \ sample.folder != sample_widget[ 'folder' ] or \ form_values.content != sample_widget[ 'field_values' ]: # Information about this sample has been changed. sample.name = sample_widget[ 'name' ] - barcode = sample_widget[ 'barcode' ] - # The bar_code field requires special handling because after a request is submitted, the - # state of a sample cannot be changed without a bar_code associated with the sample. Bar - # codes can only be added to a sample after the request is submitted. Also, a samples will - # not have an associated SampleState until the request is submitted, at which time the sample - # is automatically associated with the first SamplesState configured by the admin for the - # request's RequestType. - if barcode: - bc_message = self.__validate_barcode( trans, sample, bar_code ) + bar_code = sample_widget[ 'bar_code' ] + # If the sample has a new bar_code, make sure it is unique. + if bar_code: + bc_message = self.__validate_bar_code( trans, sample, bar_code ) if bc_message: kwd[ 'message' ] = bc_message del kwd[ 'save_samples_button' ] @@ -1191,7 +1191,7 @@ class RequestsCommon( BaseController, Us 'Bar code associated with the sample' ) trans.sa_session.add( event ) trans.sa_session.flush() - sample.bar_code = barcode + sample.bar_code = bar_code sample.library = sample_widget[ 'library' ] sample.folder = sample_widget[ 'folder' ] form_values.content = sample_widget[ 'field_values' ] @@ -1281,7 +1281,7 @@ class RequestsCommon( BaseController, Us # Update the sample attributes from kwd sample_id = None name = util.restore_text( params.get( 'sample_%i_name' % index, sample.name ) ) - bar_code = util.restore_text( params.get( 'sample_%i_barcode' % index, sample.bar_code ) ) + bar_code = util.restore_text( params.get( 'sample_%i_bar_code' % index, sample.bar_code ) ) library_id = util.restore_text( params.get( 'sample_%i_library_id' % id_index, '' ) ) if not library_id and sample.library: library_id = trans.security.encode_id( sample.library.id ) @@ -1303,7 +1303,7 @@ class RequestsCommon( BaseController, Us **kwd ) sample_widgets.append( dict( id=sample_id, name=name, - barcode=bar_code, + bar_code=bar_code, library=library, folder=folder, field_values=field_values, @@ -1317,7 +1317,7 @@ class RequestsCommon( BaseController, Us if not name: break id_index = index + 1 - bar_code = util.restore_text( params.get( 'sample_%i_barcode' % index, '' ) ) + bar_code = util.restore_text( params.get( 'sample_%i_bar_code' % index, '' ) ) library_id = util.restore_text( params.get( 'sample_%i_library_id' % id_index, '' ) ) folder_id = util.restore_text( params.get( 'sample_%i_folder_id' % id_index, '' ) ) library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) @@ -1334,7 +1334,7 @@ class RequestsCommon( BaseController, Us **kwd ) sample_widgets.append( dict( id=None, name=name, - barcode=bar_code, + bar_code=bar_code, library=library, folder=folder, field_values=field_values, @@ -1492,31 +1492,24 @@ class RequestsCommon( BaseController, Us action='edit_samples', cntrller=cntrller, **kwd ) ) - def __validate_barcode( self, trans, sample, barcode ): + def __validate_bar_code( self, trans, sample, bar_code ): """ - Makes sure that the barcode about to be assigned to a sample is globally unique. - That is, barcodes must be unique across requests in Galaxy sample tracking. + Make sure that the bar_code about to be assigned to a sample is globally unique. + That is, bar_codes must be unique across requests in Galaxy sample tracking. + Bar codes are not required, but if used, they can only be added to a sample after + the request is submitted. """ message = '' unique = True for index in range( len( sample.request.samples ) ): - # Check for empty bar code - if not barcode.strip(): - if sample.state.id == sample.request.type.states[0].id: - # The user has not yet filled in the barcode value, but the sample is - # 'new', so all is well. - break - else: - message = "Fill in the barcode for sample (%s) before changing it's state." % sample.name - break # TODO: Add a unique constraint to sample.bar_code table column # Make sure bar code is unique - for sample_with_barcode in trans.sa_session.query( trans.model.Sample ) \ - .filter( trans.model.Sample.table.c.bar_code == barcode ): - if sample_with_barcode and sample_with_barcode.id != sample.id: + for sample_with_bar_code in trans.sa_session.query( trans.model.Sample ) \ + .filter( trans.model.Sample.table.c.bar_code == bar_code ): + if sample_with_bar_code and sample_with_bar_code.id != sample.id: message = '''The bar code (%s) associated with the sample (%s) belongs to another sample. Bar codes must be unique across all samples, so use a different bar code - for this sample.''' % ( barcode, sample.name ) + for this sample.''' % ( bar_code, sample.name ) unique = False break if not unique: --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -122,7 +122,7 @@ is_rejected = request.is_rejected is_submitted = sample.request.is_submitted is_unsubmitted = sample.request.is_unsubmitted - can_delete_samples = not is_complete + can_delete_samples = editing_samples and request.samples and ( ( is_admin and not is_complete ) or is_unsubmitted ) display_checkboxes = editing_samples and ( is_complete or is_rejected or is_submitted ) display_bar_code = request.samples and ( is_complete or is_rejected or is_submitted ) display_datasets = request.samples and ( is_complete or is_submitted ) @@ -153,10 +153,10 @@ %if display_bar_code: <td valign="top"> %if is_admin: - <input type="text" name="sample_${sample_widget_index}_barcode" value="${sample_widget['barcode']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}" size="10"/> %else: - ${sample_widget['barcode']} - <input type="hidden" name="sample_${sample_widget_index}_barcode" value="${sample_widget['barcode']}"/> + ${sample_widget['bar_code']} + <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}"/> %endif </td> %endif @@ -234,7 +234,7 @@ is_submitted = request.is_submitted is_unsubmitted = request.is_unsubmitted can_add_samples = request.is_unsubmitted - can_delete_samples = editing_samples and request.samples and not is_complete + can_delete_samples = editing_samples and request.samples and ( ( is_admin and not is_complete ) or is_unsubmitted ) can_edit_samples = request.samples and ( is_admin or not is_complete ) can_select_datasets = is_admin and displayable_sample_widgets and ( is_submitted or is_complete ) can_transfer_datasets = is_admin and request.samples and not request.is_rejected @@ -280,14 +280,14 @@ <tbody><% trans.sa_session.refresh( request ) %> ## displayable_sample_widgets is a dictionary whose keys are: - ## id, name, barcode, library, folder, field_values, library_select_field, folder_select_field + ## id, name, bar_code, library, folder, field_values, library_select_field, folder_select_field ## A displayable_sample_widget will have an id == None if the widget's associated sample has not ## yet been saved (i.e., the use clicked the "Add sample" button but has not yet clicked the ## "Save" button. %for sample_widget_index, sample_widget in enumerate( displayable_sample_widgets ): <% sample_widget_name = sample_widget[ 'name' ] - sample_widget_barcode = sample_widget[ 'barcode' ] + sample_widget_bar_code = sample_widget[ 'bar_code' ] sample_widget_library = sample_widget[ 'library' ] if sample_widget_library: if cntrller == 'requests': @@ -309,7 +309,12 @@ <td> %if sample.state and ( can_select_datasets or can_transfer_datasets ): ## A sample will have a state only after the request has been submitted. - <% encoded_id = trans.security.encode_id( sample.id ) %> + <% + encoded_id = trans.security.encode_id( sample.id ) + transferred_dataset_files = sample.transferred_dataset_files + if not transferred_dataset_files: + transferred_dataset_files = [] + %><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="sample-${sample.id}-popup"> ${sample.name} </div> @@ -317,8 +322,10 @@ %if can_select_datasets: <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ), sample_id=trans.security.encode_id( sample.id ) )}">Select datasets to transfer</a></li> %endif - %if sample.untransferred_dataset_files: - <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Transfer datasets</a></li> + %if sample.datasets and len( sample.datasets ) > len( transferred_dataset_files ): + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Manage selected datasets</a></li> + %elif sample.datasets and len(sample.datasets ) == len( transferred_dataset_files ): + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ), transfer_status=trans.model.SampleDataset.transfer_status.COMPLETE )}">View transferred datasets</a></li> %endif </div> %else: @@ -326,7 +333,7 @@ %endif </td> %if display_bar_code: - <td>${sample_widget_barcode}</td> + <td>${sample_widget_bar_code}</td> %endif %if is_unsubmitted: <td>Unsubmitted</td> @@ -361,9 +368,8 @@ <td> %if is_admin: <% - if sample.transferred_dataset_files: - transferred_dataset_files = sample.transferred_dataset_files - else: + transferred_dataset_files = sample.transferred_dataset_files + if not transferred_dataset_files: transferred_dataset_files = [] %> %if not sample.datasets: --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1575,7 +1575,7 @@ class TwillTestCase( unittest.TestCase ) for index, field_value in enumerate( bar_codes ): sample_field_name = "sample_%i_name" % index sample_field_value = samples[ index ].name.replace( ' ', '+' ) - field_name = "sample_%i_barcode" % index + field_name = "sample_%i_bar_code" % index url += "&%s=%s" % ( field_name, field_value ) url += "&%s=%s" % ( sample_field_name, sample_field_value ) url += "&save_samples_button=Save"

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galaxy-dist commit f2383b761f4e: Make sure samples have associated target libraries befoe enabling ability to transfer datasets, use better naming convention for request history code and templates, eliminate the ability to submit a request unless it has samples.
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 1289507783 18000 # Node ID f2383b761f4e05442fd5ba6b1cde517732aa2c03 # Parent dfc848840870fa9936a69e62322446fcb940fb40 Make sure samples have associated target libraries befoe enabling ability to transfer datasets, use better naming convention for request history code and templates, eliminate the ability to submit a request unless it has samples. --- a/templates/requests/common/view_sample_datasets.mako +++ b/templates/requests/common/view_sample_datasets.mako @@ -7,14 +7,14 @@ is_complete = sample.request.is_complete is_submitted = sample.request.is_submitted can_select_datasets = is_admin and ( is_complete or is_submitted ) - can_transfer_datasets = is_admin and sample.untransferred_dataset_files + can_transfer_datasets = is_admin and sample.untransferred_dataset_files and sample.library and sample.folder %><br/><br/><ul class="manage-table-actions"> %if can_transfer_datasets: - <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Transfer datasets</a></li> + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Manage selected datasets</a></li> %endif <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ), transfer_status=transfer_status )}">Refresh page</a></li><li><a class="action-button" id="sample-${sample.id}-popup" class="menubutton">Dataset Actions</a></li> --- a/templates/requests/common/edit_samples.mako +++ b/templates/requests/common/edit_samples.mako @@ -47,7 +47,7 @@ %if can_edit_request: <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit this request</a> %endif - <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> %if can_reject: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> %endif --- a/lib/galaxy/web/controllers/requests.py +++ b/lib/galaxy/web/controllers/requests.py @@ -57,9 +57,9 @@ class Requests( BaseController ): action='undelete_request', cntrller='requests', **kwd ) ) - if operation == "request_events": + if operation == "view_request_history": return trans.response.send_redirect( web.url_for( controller='requests_common', - action='request_events', + action='view_request_history', cntrller='requests', **kwd ) ) --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -76,7 +76,7 @@ class RequestsGrid( grids.Grid ): StateColumn( "State", key='state', filterable="advanced", - link=( lambda item: iff( item.deleted, None, dict( operation="request_events", id=item.id ) ) ) + link=( lambda item: iff( item.deleted, None, dict( operation="view_request_history", id=item.id ) ) ) ) ] columns.append( grids.MulticolFilterColumn( "Search", @@ -579,8 +579,8 @@ class RequestsCommon( BaseController, Us status=status, message=message ) ) @web.expose - @web.require_login( "sequencing request events" ) - def request_events( self, trans, cntrller, **kwd ): + @web.require_login( "sequencing request history" ) + def view_request_history( self, trans, cntrller, **kwd ): params = util.Params( kwd ) request_id = params.get( 'id', None ) try: @@ -590,7 +590,7 @@ class RequestsCommon( BaseController, Us events_list = [] for event in request.events: events_list.append( ( event.state, time_ago( event.update_time ), event.comment ) ) - return trans.fill_template( '/requests/common/events.mako', + return trans.fill_template( '/requests/common/view_request_history.mako', cntrller=cntrller, events_list=events_list, request=request ) --- a/templates/admin/requests/select_datasets_to_transfer.mako +++ b/templates/admin/requests/select_datasets_to_transfer.mako @@ -72,7 +72,7 @@ <% is_admin = cntrller == 'requests_admin' and trans.user_is_admin() - can_transfer_datasets = is_admin and sample.untransferred_dataset_files + can_transfer_datasets = is_admin and sample.untransferred_dataset_files and sample.library and sample.folder %><br/><br/> @@ -85,8 +85,15 @@ </ul> %if not sample: + <br/><font color="red"><b><i>Select a sample before selecting datasets to transfer</i></b></font> - <br/><br/> + <br/> +%endif + +%if request.samples_without_library_destinations: + <br/> + <font color="red"><b><i>Select a target data library and folder for all samples before starting the sequence run</i></b></font> + <br/> %endif %if message: --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -175,9 +175,9 @@ class RequestsAdmin( BaseController, Use action='view_request', cntrller='requests_admin', **kwd ) ) - if operation == "request_events": + if operation == "view_request_history": return trans.response.send_redirect( web.url_for( controller='requests_common', - action='request_events', + action='view_request_history', cntrller='requests_admin', **kwd ) ) if operation == "reject": --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1517,7 +1517,7 @@ class TwillTestCase( unittest.TestCase ) for check_str in strings_not_displayed: self.check_string_not_in_page( check_str ) def view_request_history( self, cntrller, request_id, strings_displayed=[], strings_not_displayed=[] ): - self.visit_url( "%s/requests_common/request_events?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) ) + self.visit_url( "%s/requests_common/view_request_history?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) ) for check_str in strings_displayed: self.check_page_for_string( check_str ) for check_str in strings_not_displayed: --- a/templates/requests/common/events.mako +++ /dev/null @@ -1,53 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<% - is_admin = cntrller == 'requests_admin' and trans.user_is_admin() - can_edit_request = ( is_admin and not request.is_complete ) or request.is_unsubmitted - can_reject_request = is_admin and request.is_submitted - can_add_samples = request.is_unsubmitted -%> - -<br/><br/> -<ul class="manage-table-actions"> - <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request Actions</a></li> - <div popupmenu="request-${request.id}-popup"> - <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> - %if can_edit_request: - <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit this request</a> - %endif - %if can_add_samples: - <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit this request</a> - %endif - %if can_reject_request: - <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> - %endif - </div> -</ul> - -%if message: - ${render_msg( message, status )} -%endif - -<h2>History of Sequencing Request "${request.name}"</h2> - -<div class="toolForm"> - <table class="grid"> - <thead> - <tr> - <th>State</th> - <th>Last Update</th> - <th>Comments</th> - </tr> - </thead> - <tbody> - %for state, updated, comments in events_list: - <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - <td><b><a>${state}</a></b></td> - <td><a>${updated}</a></td> - <td><a>${comments}</a></td> - </tr> - %endfor - </tbody> - </table> -</div> --- a/templates/requests/common/edit_basic_request_info.mako +++ b/templates/requests/common/edit_basic_request_info.mako @@ -3,7 +3,13 @@ <% is_admin = cntrller == 'requests_admin' and trans.user_is_admin() - can_add_samples = request.is_unsubmitted + is_complete = request.is_complete + is_submitted = request.is_submitted + is_unsubmitted = request.is_unsubmitted + can_add_samples = is_unsubmitted + can_reject = is_admin and is_submitted + can_select_datasets = is_admin and ( is_complete or is_submitted ) + can_submit_request = request.samples and is_unsubmitted %><br/><br/> @@ -11,12 +17,14 @@ <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request Actions</a></li><div popupmenu="request-${request.id}-popup"><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> - %if can_add_samples: + %if can_submit_request: <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit this request</a> %endif - <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> - %if is_admin and request.is_submitted: + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> + %if can_reject: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> + %endif + %if can_select_datasets: <a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> %endif </div> --- a/templates/admin/requests/reject.mako +++ b/templates/admin/requests/reject.mako @@ -8,7 +8,7 @@ <h2>Reject Sequencing Request "${request.name}"</h2><ul class="manage-table-actions"><li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id(request.id) )}">View history</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id(request.id) )}">View history</a></li><li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id(request.id) )}">Browse this request</a> --- a/templates/requests/common/view_request.mako +++ b/templates/requests/common/view_request.mako @@ -44,7 +44,7 @@ %if can_edit_request: <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit this request</a> %endif - <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> %if can_reject: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> %endif @@ -52,8 +52,15 @@ </ul> %if request.is_rejected: + <br/><font color="red"><b><i>Reason for rejection: </i></b></font><b>${request.last_comment}</b> - <br/><br/> + <br/> +%endif + +%if request.samples_without_library_destinations: + <br/> + <font color="red"><b><i>Select a target data library and folder for all samples before starting the sequence run</i></b></font> + <br/> %endif %if message: @@ -94,7 +101,7 @@ <div class="form-row"><label>${field_label}:</label> %if field_label == 'State': - <a href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">${field_value}</a> + <a href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">${field_value}</a> %else: ${field_value} %endif @@ -154,6 +161,11 @@ render_buttons = can_edit_samples %> ${render_samples_grid( cntrller, request, displayable_sample_widgets=displayable_sample_widgets, action='view_request', editing_samples=False, encoded_selected_sample_ids=[], render_buttons=render_buttons, grid_header=grid_header )} + ## Render the other grids + <% trans.sa_session.refresh( request.type.sample_form ) %> + %for grid_index, grid_name in enumerate( request.type.sample_form.layout ): + ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, editing_samples=False )} + %endfor %else: There are no samples. %if can_add_samples: @@ -162,8 +174,3 @@ </ul> %endif %endif -## Render the other grids -<% trans.sa_session.refresh( request.type.sample_form ) %> -%for grid_index, grid_name in enumerate( request.type.sample_form.layout ): - ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, editing_samples=False )} -%endfor --- /dev/null +++ b/templates/requests/common/view_request_history.mako @@ -0,0 +1,58 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<% + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + is_complete = request.is_complete + is_submitted = request.is_submitted + is_unsubmitted = request.is_unsubmitted + can_add_samples = is_unsubmitted + can_edit_request = ( is_admin and not is_complete ) or is_unsubmitted + can_reject = is_admin and is_submitted + can_select_datasets = is_admin and ( is_complete or is_submitted ) + can_submit_request = request.samples and is_unsubmitted +%> + +<br/><br/> +<ul class="manage-table-actions"> + <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request Actions</a></li> + <div popupmenu="request-${request.id}-popup"> + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> + %if can_edit_request: + <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit this request</a> + %endif + %if can_submit_request: + <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit this request</a> + %endif + %if can_reject: + <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> + %endif + </div> +</ul> + +%if message: + ${render_msg( message, status )} +%endif + +<h2>History of sequencing request "${request.name}"</h2> + +<div class="toolForm"> + <table class="grid"> + <thead> + <tr> + <th>State</th> + <th>Last Update</th> + <th>Comments</th> + </tr> + </thead> + <tbody> + %for state, updated, comments in events_list: + <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> + <td><b><a>${state}</a></b></td> + <td><a>${updated}</a></td> + <td><a>${comments}</a></td> + </tr> + %endfor + </tbody> + </table> +</div> --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -322,7 +322,7 @@ %if can_select_datasets: <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ), sample_id=trans.security.encode_id( sample.id ) )}">Select datasets to transfer</a></li> %endif - %if sample.datasets and len( sample.datasets ) > len( transferred_dataset_files ): + %if sample.datasets and len( sample.datasets ) > len( transferred_dataset_files ) and sample.library and sample.folder: <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Manage selected datasets</a></li> %elif sample.datasets and len(sample.datasets ) == len( transferred_dataset_files ): <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ), transfer_status=trans.model.SampleDataset.transfer_status.COMPLETE )}">View transferred datasets</a></li>

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galaxy-dist commit 0f6ace5c397b: Ignore backup files from some editors
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 peterjc <p.j.a.cock(a)googlemail.com> # Date 1286965717 -3600 # Node ID 0f6ace5c397b000993db8e491a33e42423cdc807 # Parent d8184d91928c83f0269bd0267be949bc5d676e8b Ignore backup files from some editors --- a/.hgignore +++ b/.hgignore @@ -43,4 +43,4 @@ run_functional_tests.html *.orig .DS_Store *.rej - +*~

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galaxy-dist commit d8184d91928c: Remove FASTA filter script from BLAST+ tools (I want to generalise it)
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 peterjc <p.j.a.cock(a)googlemail.com> # Date 1287998919 -3600 # Node ID d8184d91928c83f0269bd0267be949bc5d676e8b # Parent 5c212dfc6189bb41d334b0519411ca4f04fde9ec Remove FASTA filter script from BLAST+ tools (I want to generalise it) --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -269,7 +269,6 @@ <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /><tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /><tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /> - <tool file="ncbi_blast_plus/blast_filter_fasta.xml" /></section><section name="NGS: Mapping" id="solexa_tools"><tool file="sr_mapping/lastz_wrapper.xml" /> --- a/tools/ncbi_blast_plus/blast_filter_fasta.py +++ /dev/null @@ -1,38 +0,0 @@ -#!/usr/bin/env python -"""Filter a FASTA file using tabular output, e.g. from BLAST. - -Takes five command line options, tabular BLAST filename, ID column number -(using one based counting), input FASTA filename, and two output FASTA -filenames (for records with and without any BLAST hits). - -In the default NCBI BLAST+ tabular output, the query sequence ID is in column -one, and the ID of the match from the database is in column two. -""" -import sys -from galaxy_utils.sequence.fasta import fastaReader, fastaWriter - -#Parse Command Line -blast_file, blast_col, in_file, out_positive_file, out_negative_file = sys.argv[1:] -blast_col = int(blast_col)-1 -assert blast_col >= 0 - -#Read tabular BLAST file and record all queries with hit(s) -ids = set() -blast_handle = open(blast_file, "rU") -for line in blast_handle: - ids.add(line.split("\t")[blast_col]) -blast_handle.close() - -#Write filtered FASTA file based on IDs from BLAST file -reader = fastaReader(open(in_file, "rU")) -positive_writer = fastaWriter(open(out_positive_file, "w")) -negative_writer = fastaWriter(open(out_negative_file, "w")) -for record in reader: - #The [1:] is because the fastaReader leaves the > on the identifer. - if record.identifier and record.identifier.split()[0][1:] in ids: - positive_writer.write(record) - else: - negative_writer.write(record) -positive_writer.close() -negative_writer.close() -reader.close() --- a/tools/ncbi_blast_plus/blast_filter_fasta.xml +++ /dev/null @@ -1,37 +0,0 @@ -<tool id="blast_filter_fasta" name="Filter FASTA using BLAST output" version="0.0.1"> - <description>Divide a FASTA file based on BLAST hits</description> - <command interpreter="python"> - blast_filter_fasta.py $blast_file $blast_col $in_file $out_positive_file $out_negative_file - </command> - <inputs> - <param name="in_file" type="data" format="fasta" label="FASTA file to filter"/> - <param name="blast_file" type="data" format="tabular" label="Tabular BLAST output"/> - <param name="blast_col" type="select" label="Column containing FASTA identifiers"> - <option value="1">Column 1 - BLAST query ID</option> - <option value="2">Column 2 - BLAST match ID</option> - </param> - </inputs> - <outputs> - <data name="out_positive_file" format="fasta" label="Sequences with BLAST hits" /> - <data name="out_negative_file" format="fasta" label="Sequences without BLAST hits" /> - </outputs> - <requirements> - </requirements> - <tests> - </tests> - <help> - -**What it does** - -Typical use would be to take a multi-sequence FASTA and the tabular output of -running BLAST on it, and divide the FASTA file in two: those sequence with a -BLAST hit, and those without. - -In the default NCBI BLAST+ tabular output, the query sequence ID is in column -one, and the ID of the match from the database is in column two. - -This allows you to filter the FASTA file for the subjects in the BLAST search, -rather than filtering the FASTA file for the queries in the BLAST search. - - </help> -</tool>

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galaxy-dist commit 5c212dfc6189: Fix a caption capitalisation
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 peterjc <p.j.a.cock(a)googlemail.com> # Date 1286980710 -3600 # Node ID 5c212dfc6189bb41d334b0519411ca4f04fde9ec # Parent 122aaabe2c7eb48726f65233370926b838b6b444 Fix a caption capitalisation --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -62,7 +62,7 @@ blastn <option value="vecscreen">vecscreen</option> --></param> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="-outfmt 6" selected="True">Tabular</option><option value="-outfmt 5">BLAST XML</option> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -57,7 +57,7 @@ blastp <option value="blastp">blastp</option><option value="blastp-short">blastp-short</option></param> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="-outfmt 6" selected="True">Tabular</option><option value="-outfmt 5">BLAST XML</option> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -51,7 +51,7 @@ tblastx <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/></when></conditional> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="-outfmt 6" selected="True">Tabular</option><option value="-outfmt 5">BLAST XML</option> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -52,7 +52,7 @@ blastx <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/></when></conditional> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="-outfmt 6" selected="True">Tabular</option><option value="-outfmt 5">BLAST XML</option> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -52,7 +52,7 @@ tblastn <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/></when></conditional> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="-outfmt 6" selected="True">Tabular</option><option value="-outfmt 5">BLAST XML</option>

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galaxy-dist commit 10d0ffe5b7e2: Include BLAST-XML to tabular in tool_conf.xml.sample
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 peterjc <p.j.a.cock(a)googlemail.com> # Date 1286962559 -3600 # Node ID 10d0ffe5b7e22b2d122945ab5b7fa951a18c6e4a # Parent caed55b53f5a811226e0bfa1c177e7b3e57a909a Include BLAST-XML to tabular in tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -268,6 +268,7 @@ <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" /><tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /><tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /> + <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /><tool file="ncbi_blast_plus/blast_filter_fasta.xml" /></section><section name="NGS: Mapping" id="solexa_tools">

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