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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 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 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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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"

1 0

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" />

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galaxy-dist commit ff7327f2946e: When generating the list of target libraries for transferring sample datasets, use all libraries accessible to the request's user rather than all libraries for which that user has LIBRARY_ADD permission.
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 1289522279 18000 # Node ID ff7327f2946e9121139cefbf4a45dba2791b7162 # Parent f2383b761f4e05442fd5ba6b1cde517732aa2c03 When generating the list of target libraries for transferring sample datasets, use all libraries accessible to the request's user rather than all libraries for which that user has LIBRARY_ADD permission. --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -53,6 +53,8 @@ class User( object ): roles.append( role ) return roles def accessible_libraries( self, trans, actions ): + # TODO: eliminate this method - instead use + # trans.app.security_agent.get_accessible_libraries(). # Get all permitted libraries for this user all_libraries = trans.sa_session.query( trans.app.model.Library ) \ .filter( trans.app.model.Library.table.c.deleted == False ) \ --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -2,6 +2,7 @@ from galaxy.web.base.controller import * from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.model.orm import * from galaxy import model, util +from galaxy.util.odict import odict from galaxy.web.form_builder import * import logging, os, csv @@ -413,8 +414,7 @@ class RequestsCommon( BaseController, Us cntrller=cntrller, id=request_id, editing_samples=editing_samples ) ) - # Get all libraries for which the current user has permission to add items. - libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) + libraries = self.__get_accessible_libraries( trans, request.user ) # Build a list of sample widgets (based on the attributes of each sample) for display. displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd ) encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) @@ -815,8 +815,7 @@ class RequestsCommon( BaseController, Us else: sample_index = len( displayable_sample_widgets ) if params.get( 'add_sample_button', False ): - # Get all libraries for which the current user has permission to add items - libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) + libraries = self.__get_accessible_libraries( trans, request.user ) num_samples_to_add = int( params.get( 'num_sample_to_copy', 1 ) ) # See if the user has selected a sample to copy. copy_sample_index = int( params.get( 'copy_sample_index', -1 ) ) @@ -1186,9 +1185,9 @@ class RequestsCommon( BaseController, Us # the first time a bar code was added to the sample, so change it's state # to the next associated SampleState. if sample.state.id == request.type.states[0].id: - event = trans.app.model.SampleEvent(sample, - request.type.states[1], - 'Bar code associated with the sample' ) + event = trans.model.SampleEvent( sample, + request.type.states[1], + 'Bar code associated with the sample' ) trans.sa_session.add( event ) trans.sa_session.flush() sample.bar_code = bar_code @@ -1216,6 +1215,19 @@ class RequestsCommon( BaseController, Us folder = None return library, folder # ===== Methods for handling form definition widgets ===== + def __get_accessible_libraries( self, trans, user ): + # Return a dictionary whose keys are libraries that user can + # access and whose values are empty string ''. This is because + # methods expect the dictionary instead of a simple list because + # this method replaces the deprecated model.User.accessible_libraries() + # method. TODO: fix methods that call this method to expect the list + # returne dby trans.app.securoty_agent.get_accessible_libraries() and + # then eliminate this method. + accessible_libraries = trans.app.security_agent.get_accessible_libraries( trans, user ) + accessible_libraries_dict = odict() + for library in accessible_libraries: + accessible_libraries_dict[ library ] = '' + return accessible_libraries_dict def __get_request_widgets( self, trans, id ): """Get the widgets for the request""" request = trans.sa_session.query( trans.model.Request ).get( id ) @@ -1263,8 +1275,7 @@ class RequestsCommon( BaseController, Us # Build the list of widgets which will be used to render each sample row on the request page if not request: return sample_widgets - # Get the list of libraries for which the current user has permission to add items. - libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) + libraries = self.__get_accessible_libraries( trans, request.user ) # Build the list if sample widgets, populating the values from kwd. for index, sample in enumerate( samples ): id_index = index + 1 --- a/lib/galaxy/webapps/community/__init__.py +++ b/lib/galaxy/webapps/community/__init__.py @@ -1,3 +1,3 @@ -"""The Galaxy Reports application.""" +"""The Galaxy Tool Shed application.""" from galaxy.web.framework import expose, url_for --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -74,6 +74,8 @@ class RBACAgent: raise "Unimplemented Method" def make_library_public( self, library ): raise "Unimplemented Method" + def get_accessible_libraries( self, trans, user ): + raise "Unimplemented Method" def folder_is_public( self, library ): raise "Unimplemented Method" def make_folder_public( self, folder, count=0 ): @@ -244,6 +246,26 @@ class GalaxyRBACAgent( RBACAgent ): return self.allow_action( roles, self.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset ) def can_access_library( self, roles, library ): return self.library_is_public( library ) or self.allow_action( roles, self.permitted_actions.LIBRARY_ACCESS, library ) + def get_accessible_libraries( self, trans, user ): + """Return all data libraries that user can access""" + accessible_libraries = [] + current_user_role_ids = [ role.id for role in user.all_roles() ] + library_access_action = self.permitted_actions.LIBRARY_ACCESS.action + restricted_library_ids = [ lp.library_id for lp in trans.sa_session.query( trans.model.LibraryPermissions ) \ + .filter( trans.model.LibraryPermissions.table.c.action == library_access_action ) \ + .distinct() ] + accessible_restricted_library_ids = [ lp.library_id for lp in trans.sa_session.query( trans.model.LibraryPermissions ) \ + .filter( and_( trans.model.LibraryPermissions.table.c.action == library_access_action, + trans.model.LibraryPermissions.table.c.role_id.in_( current_user_role_ids ) ) ) ] + # Filter to get libraries accessible by the current user. Get both + # public libraries and restricted libraries accessible by the current user. + for library in trans.sa_session.query( trans.model.Library ) \ + .filter( and_( trans.model.Library.table.c.deleted == False, + ( or_( not_( trans.model.Library.table.c.id.in_( restricted_library_ids ) ), + trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) ) ) ) \ + .order_by( trans.app.model.Library.name ): + accessible_libraries.append( library ) + return accessible_libraries def can_access_library_item( self, roles, item, user ): if type( item ) == self.model.Library: return self.can_access_library( roles, item )

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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 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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