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galaxy-dist commit d4b85e30e56d: sample tracking
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1287147090 14400 # Node ID d4b85e30e56d605edc2236ccba5cde41bda1510a # Parent fb2a31820ccff6f02bb24a0632f214bfef0a8b0a sample tracking - create request search+select box bug fixed. - sample datasets grid operations fixed --- a/templates/requests/common/sample_datasets.mako +++ b/templates/requests/common/sample_datasets.mako @@ -1,5 +1,5 @@ <%def name="render_sample_datasets( sample )"> - ${len( sample.transferred_dataset_files )}/${len( sample.datasets )} + ${len( sample.transferred_dataset_files )} / ${len( sample.datasets )} </%def> ${render_sample_datasets( sample )} --- a/templates/requests/common/create_request.mako +++ b/templates/requests/common/create_request.mako @@ -21,7 +21,7 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Create a new request</div> + <div class="toolFormTitle">Create a new sequencing request</div> %if len( request_type_select_field.options ) == 1: There are no sequencer configurations available for ${trans.user.email} to create sequencing requests. %else: --- a/templates/admin/requests/get_data.mako +++ b/templates/admin/requests/get_data.mako @@ -104,7 +104,9 @@ <option value="${f}">${f}</option> %endfor </select> - <br/> + </div> + <div class="form-row"> + <div id="file_details" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div></div><div class="form-row"><input type="submit" name="select_show_datasets_button" value="Select & show datasets"/> --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -140,9 +140,20 @@ class RequestsCommon( BaseController, Us request_type = None # user_id will not be 'none' if an admin user is submitting this request on behalf of another user # and they selected that user's id from the user_id SelectField. + user_id_encoded = True user_id = params.get( 'user_id', 'none' ) if user_id != 'none': - user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) + try: + user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) + except TypeError, e: + # We must have an email address rather than an encoded user id + # This is because the galaxy.base.js creates a search+select box + # when there are more than 20 items in a selectfield + user = trans.sa_session.query( trans.model.User ) \ + .filter( trans.model.User.table.c.email==util.restore_text( user_id ) ) \ + .first() + user_id_encoded = False + elif not is_admin: user = trans.user else: @@ -152,6 +163,9 @@ class RequestsCommon( BaseController, Us if is_admin and user_id == 'none': message = 'Select the user on behalf of whom you are submitting this request.' status = 'error' + elif user is None: + message = 'Invalid user ID (%s)' % str(user_id) + status = 'error' elif not name: message = 'Enter the name of the request.' status = 'error' @@ -170,10 +184,6 @@ class RequestsCommon( BaseController, Us widgets = [] if request_type is not None or status == 'error': # Either the user selected a request_type or an error exists on the form. - if is_admin: - widgets.append( dict( label='Select user', - widget=self.__build_user_id_select_field( trans, selected_value=user_id ), - helptext='Submit the request on behalf of the selected user (Required)')) widgets.append( dict( label='Name of the Experiment', widget=TextField( 'name', 40, util.restore_text( params.get( 'name', '' ) ) ), helptext='(Required)') ) @@ -182,9 +192,20 @@ class RequestsCommon( BaseController, Us helptext='(Optional)') ) if request_type is not None: widgets += request_type.request_form.get_widgets( user, **kwd ) - # In case there is an error on the form, make sure to populate widget fields with anything the user - # may have already entered. - self.populate_widgets_from_kwd( trans, widgets, **kwd ) + # In case there is an error on the form, make sure to populate widget fields with anything the user + # may have already entered. + self.populate_widgets_from_kwd( trans, widgets, **kwd ) + if request_type is not None or status == 'error': + # Either the user selected a request_type or an error exists on the form. + if is_admin: + if not user_id_encoded: + selected_user_id = trans.security.encode_id( user.id ) + else: + selected_user_id = user_id + user_widget = dict( label='Select user', + widget=self.__build_user_id_select_field( trans, selected_value=selected_user_id ), + helptext='Submit the request on behalf of the selected user (Required)') + widgets = [ user_widget ] + widgets return trans.fill_template( '/requests/common/create_request.mako', cntrller=cntrller, request_type_select_field=request_type_select_field, @@ -873,7 +894,7 @@ class RequestsCommon( BaseController, Us # Build the library_select_field and folder_select_field for the new sample being added. library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans, user=request.user, - sample_index=sample_index, + sample_index=len( current_samples ), libraries=libraries, sample=None, library_id=library_id, --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -184,23 +184,6 @@ class RequestsAdmin( BaseController, Use **kwd ) ) # Render the list view return self.request_grid( trans, **kwd ) - @web.json - def get_file_details( self, trans, id, folder_path ): - def print_ticks( d ): - # pexpect timeout method - pass - # Avoid caching - trans.response.headers['Pragma'] = 'no-cache' - trans.response.headers['Expires'] = '0' - request = trans.sa_session.query( trans.model.Request ).get( int( id ) ) - datatx_info = request.type.datatx_info - cmd = 'ssh %s@%s "ls -oghp \'%s\'"' % ( datatx_info['username'], - datatx_info['host'], - folder_path ) - output = pexpect.run( cmd, - events={ '.ssword:*' : datatx_info[ 'password'] + '\r\n', pexpect.TIMEOUT : print_ticks }, - timeout=10 ) - return unicode( output.replace( '\n', '<br/>' ) ) @web.expose @web.require_admin def reject( self, trans, **kwd ): @@ -244,11 +227,6 @@ class RequestsAdmin( BaseController, Use params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - sample_id = params.get( 'sample_id', None ) - try: - sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id ( sample_id ) ) - except: - return invalid_id_redirect( trans, 'requests_admin', sample_id ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() sample_dataset_id = params.get( 'id', None ) @@ -268,7 +246,9 @@ class RequestsAdmin( BaseController, Use not_deleted = [] for sample_dataset in selected_sample_datasets: # Make sure the dataset has been transferred before deleting it. - if sample_dataset in sample.untransferred_dataset_files: + if sample_dataset in sample_dataset.sample.untransferred_dataset_files: + # save the sample to which these datasets belong to + sample = sample_dataset.sample trans.sa_session.delete( sample_dataset ) trans.sa_session.flush() else: @@ -279,7 +259,7 @@ class RequestsAdmin( BaseController, Use message = message + ' %s could not be deleted because their transfer status is not "Not Started". ' % str( not_deleted ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_datasets', - sample_id=sample_id, + sample_id=trans.security.encode_id( sample.id ), status=status, message=message ) ) elif operation == "rename": @@ -288,7 +268,7 @@ class RequestsAdmin( BaseController, Use # has not yet been transferred. no_datasets_transferred = True for selected_sample_dataset in selected_sample_datasets: - if selected_sample_dataset in sample.untransferred_dataset_files: + if selected_sample_dataset in selected_sample_dataset.sample.untransferred_dataset_files: no_datasets_transferred = False break if no_datasets_transferred: @@ -296,15 +276,20 @@ class RequestsAdmin( BaseController, Use message = 'A dataset can be renamed only if it is in the "Not Started" state.' return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_datasets', - sample_id=sample_id, + sample_id=trans.security.encode_id( selected_sample_datasets[0].sample.id ), status=status, message=message ) ) return trans.fill_template( '/admin/requests/rename_datasets.mako', - sample=sample, + sample=selected_sample_datasets[0].sample, id_list=id_list ) elif operation == "start transfer": - self.__start_datatx( trans, sample, selected_sample_datasets ) + self.__start_datatx( trans, selected_sample_datasets[0].sample, selected_sample_datasets ) # Render the grid view + sample_id = params.get( 'sample_id', None ) + try: + sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id ( sample_id ) ) + except: + return invalid_id_redirect( trans, 'requests_admin', sample_id ) request_id = trans.security.encode_id( sample.request.id ) library_id = trans.security.encode_id( sample.library.id ) self.datatx_grid.title = 'Datasets of sample "%s"' % sample.name @@ -395,6 +380,10 @@ class RequestsAdmin( BaseController, Use if folder_path[-1] == os.sep: folder_path = os.path.dirname( folder_path[:-1] ) folder_path = self.__check_path( folder_path ) + elif params.get( 'open_folder', False ): + if len(selected_files) == 1: + folder_path = os.path.join(folder_path, selected_files[0]) + folder_path = self.__check_path( folder_path ) elif params.get( 'select_show_datasets_button', False ) or params.get( 'select_more_button', False ): # get the sample these datasets are associated with try: @@ -443,8 +432,26 @@ class RequestsAdmin( BaseController, Use status=status, message=message ) @web.json + def get_file_details( self, trans, id, folder_path ): + def print_ticks( d ): + # pexpect timeout method + pass + # Avoid caching + trans.response.headers['Pragma'] = 'no-cache' + trans.response.headers['Expires'] = '0' + request = trans.sa_session.query( trans.model.Request ).get( int( id ) ) + datatx_info = request.type.datatx_info + cmd = 'ssh %s@%s "ls -oghp \'%s\'"' % ( datatx_info['username'], + datatx_info['host'], + folder_path ) + output = pexpect.run( cmd, + events={ '.ssword:*' : datatx_info[ 'password'] + '\r\n', pexpect.TIMEOUT : print_ticks }, + timeout=10 ) + return unicode( output.replace( '\n', '<br/>' ) ) + @web.json def open_folder( self, trans, id, folder_path ): def print_ticks( d ): + # pexpect timeout method pass # Avoid caching trans.response.headers['Pragma'] = 'no-cache' --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -340,8 +340,7 @@ class UsesFormDefinitionWidgets: widget_dict[ 'widget' ] = widget else: # An existing address object was selected - address_obj = trans.sa_session.query( trans.app.model.UserAddress ).get( int( value ) ) - widget_dict[ 'widget' ] = address_obj + widget_dict[ 'widget' ] = widget # Populate the AddressField params with the form field contents widget_params_dict = {} for field_name, label, help_text in widget.fields():

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galaxy-dist commit 7c80b7c2aa6a: Add descriptive labels to output dataset names for MACS peakcalling tool.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg <dan(a)bx.psu.edu> # Date 1287508435 14400 # Node ID 7c80b7c2aa6aef5fba1b3a08e6426f5c84a125b4 # Parent 9c80bcb0bfa49d553428aca22043a8a68f773c65 Add descriptive labels to output dataset names for MACS peakcalling tool. --- a/tools/peak_calling/macs_wrapper.xml +++ b/tools/peak_calling/macs_wrapper.xml @@ -74,22 +74,22 @@ <param name="futurefdr" label="Perform the new peak detection method (futurefdr)" type="boolean" truevalue="--futurefdr" falsevalue="" checked="False" help="The default method only consider the peak location, 1k, 5k, and 10k regions in the control data; whereas the new future method also consider the 5k, 10k regions in treatment data to calculate local bias."/></inputs><outputs> - <data name="output_bed_file" format="bed"/> - <data name="output_xls_to_interval_peaks_file" format="interval"> + <data name="output_bed_file" format="bed" label="${tool.name} on ${on_string} (peaks: bed)"/> + <data name="output_xls_to_interval_peaks_file" format="interval" label="${tool.name} on ${on_string} (peaks: interval)"><filter>xls_to_interval is True</filter></data> - <data name="output_xls_to_interval_negative_peaks_file" format="interval"> + <data name="output_xls_to_interval_negative_peaks_file" format="interval" label="${tool.name} on ${on_string} (negative peaks: interval)"><filter>xls_to_interval is True</filter><filter>input_type['input_control_file1'] is not None</filter></data> - <data name="output_treatment_wig_file" format="wig"> + <data name="output_treatment_wig_file" format="wig" label="${tool.name} on ${on_string} (treatment: wig)"><filter>wig_type['wig_type_selector']=='wig'</filter></data> - <data name="output_control_wig_file" format="wig"> + <data name="output_control_wig_file" format="wig" label="${tool.name} on ${on_string} (control: wig)"><filter>wig_type['wig_type_selector'] == 'wig'</filter><filter>input_type['input_control_file1'] is not None</filter></data> - <data name="output_extra_files" format="html"/> + <data name="output_extra_files" format="html" label="${tool.name} on ${on_string} (html report)"/></outputs><configfiles><configfile name="options_file"><%

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galaxy-dist commit e029c860e717: Added tests and more help to mutation visualization tool
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1287517130 14400 # Node ID e029c860e71710d69f725e5c136b7e55fa529a42 # Parent 7c80b7c2aa6aef5fba1b3a08e6426f5c84a125b4 Added tests and more help to mutation visualization tool --- a/tools/mutation/visualize.xml +++ b/tools/mutation/visualize.xml @@ -37,16 +37,42 @@ <outputs><data format="svg" name="out_file1" /></outputs> + <tests> + <test> + <param name="input1" value="mutation_data1.txt" ftype="tabular" /> + <param name="position_col" value="2" /> + <param name="ref_col" value="4" /> + <param name="zoom_value" value="interactive" /> + <param name="name" value="s1" /> + <param name="a_col" value="5" /> + <param name="totals_col" value="9" /> + <output name="output" file="mutation_data1_interactive.svg" ftype="svg" /> + </test> + <test> + <param name="input1" value="mutation_data1.txt" ftype="tabular" /> + <param name="position_col" value="2" /> + <param name="ref_col" value="4" /> + <param name="zoom_value" value="3" /> + <param name="name" value="s1" /> + <param name="a_col" value="5" /> + <param name="totals_col" value="9" /> + <output name="output" file="mutation_data1_zoom3x.svg" ftype="svg" /> + </test> + </tests><help> **Example** - +This tool allows you to visualize mutations described in a tabular input file. It generates an SVG image which can be viewed in any web browser. + Given the input file:: gm blood gm cheek chrM 72 73 G 26394 4 49 0 26447 26398 1 23389 3 45 0 23437 23392 1 chrM 149 150 T 11 50422 2 96 50531 50435 1 4 45417 1 65 45487 45422 1 + +You will need to specify the position and reference columns in the input file. Then click on the 'Add new Sample' to add samples in the input file that you would like to visualize. For each sample you select, specify the column for base 'A' and the totals column. +This tool assumes the columns specifying bases A, C, G, T are placed consecutively and in that order in an input file. Visualization: @@ -54,7 +80,7 @@ Visualization: :width: 150 Interactivity:: - If interactive zoom/pan option is checked then the resultant image can be zoomed in or out: scroll mouse wheel; pan: drag using left mouse button. + If interactive zoom option is selected, then the resultant image can be zoomed in or out using the scroll mouse wheel and can be panned by dragging the image using left mouse button. </help></tool> --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -134,6 +134,7 @@ <tool file="visualization/GMAJ.xml" /><tool file="visualization/build_ucsc_custom_track.xml" /><tool file="maf/vcf_to_maf_customtrack.xml" /> + <tool file="mutation/visualize.xml" /></section><section name="Regional Variation" id="regVar"><tool file="regVariation/windowSplitter.xml" /> --- a/tools/mutation/visualize.py +++ b/tools/mutation/visualize.py @@ -367,7 +367,6 @@ if __name__ == '__main__': parser.add_option('-z', '--zoom', dest='zoom', action='store', default='1') parser.add_option('-p', '--position_col', dest='position_col', action='store', default='c0') parser.add_option('-r', '--ref_col', dest='ref_col', action='store', default='c1') - #parser.add_option('-n', '--interactive', dest='interactive', action='store_false', default='True') (opts, args) = parser.parse_args() mainsvg(opts, args) sys.exit(1)

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galaxy-dist commit 5f4ad3738071: trackster: Fix ReferenceTrack not drawing, summary_tree display is now histogram and more fine grained. Small overview fix, UI tweaks
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 1287007196 14400 # Node ID 5f4ad373807158f8b2ac0bcaafab9f57b972e562 # Parent 76f09e5ccb85569b56e66676e4c761f4348336fc trackster: Fix ReferenceTrack not drawing, summary_tree display is now histogram and more fine grained. Small overview fix, UI tweaks --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -292,7 +292,7 @@ var View = function( container, chrom, t view.low = Math.max(low, 0); view.high = Math.min(high, view.max_high); } - view.overview_viewport.find("canvas").remove(); + view.reset_overview(); view.redraw(); }, @@ -438,6 +438,13 @@ var View = function( container, chrom, t this.low = Math.round(cur_center - new_half); this.high = Math.round(cur_center + new_half); this.redraw(); + }, + reset_overview: function() { + this.overview_viewport.find("canvas").remove(); + this.overview_viewport.height(this.default_overview_height); + this.overview_box.height(this.default_overview_height); + this.overview_close.hide(); + this.overview_highlight.hide(); } }); @@ -648,8 +655,6 @@ var TiledTrack = function() { }, 50); }, set_overview: function() { var view = this.view; - view.overview_viewport.height(view.default_overview_height); - view.overview_box.height(view.default_overview_height); if (this.initial_canvas && this.is_overview) { view.overview_close.show(); @@ -695,6 +700,7 @@ var ReferenceTrack = function (view) { Track.call( this, null, view, view.top_labeltrack ); TiledTrack.call( this ); + this.left_offset = 200; this.height_px = 12; this.container_div.addClass( "reference-track" ); this.dummy_canvas = $("<canvas></canvas>").get(0).getContext("2d"); @@ -752,8 +758,9 @@ var ReferenceTrack = function (view) { }); for (var c = 0, str_len = seq.length; c < str_len; c++) { - var c_start = Math.round(c * w_scale); - ctx.fillText(seq[c], c_start + this.left_offset, 10); + var c_start = Math.round(c * w_scale), + gap = Math.round(w_scale / 2); + ctx.fillText(seq[c], c_start + this.left_offset + gap, 10); } parent_element.append(canvas); return canvas; @@ -991,7 +998,7 @@ var FeatureTrack = function ( name, view this.showing_details = false; this.vertical_detail_px = 10; this.vertical_nodetail_px = 2; - this.summary_draw_height = 20; + this.summary_draw_height = 30; this.default_font = "9px Monaco, Lucida Console, monospace"; this.inc_slots = {}; this.data_queue = {}; @@ -1194,32 +1201,25 @@ var FeatureTrack = function ( name, view ctx.textAlign = "right"; if (result.dataset_type == "summary_tree") { - var color, - min_color = 55, - color_span = 255 - min_color, - color_cutoff = color_span*2/3, // Where text switches from black to white - points = result.data, + var points = result.data, max = result.max, avg = result.avg, delta_x_px = Math.ceil(result.delta * w_scale); - + for ( var i = 0, len = points.length; i < len; i++ ) { var x = Math.floor( (points[i][0] - tile_low) * w_scale ); var y = points[i][1]; - + if (!y) { continue; } - color = Math.floor( color_span - (y / max) * color_span ); - ctx.fillStyle = "rgb(" +color+ "," +color+ "," +color+ ")"; - ctx.fillRect(x + left_offset, 0, delta_x_px, this.summary_draw_height); - + var y_px = y / max * this.summary_draw_height; + + ctx.fillStyle = "black"; + ctx.fillRect(x + left_offset, this.summary_draw_height - y_px, delta_x_px, y_px); + if (this.prefs.show_counts && ctx.measureText(y).width < delta_x_px) { - if (color > color_cutoff) { - ctx.fillStyle = "black"; - } else { - ctx.fillStyle = "#ddd"; - } + ctx.fillStyle = "#bbb"; ctx.textAlign = "center"; - ctx.fillText(y, x + left_offset + (delta_x_px/2), 12); + ctx.fillText(y, x + left_offset + (delta_x_px/2), this.summary_draw_height - 5); } } cur_mode = "Summary"; @@ -1252,18 +1252,19 @@ var FeatureTrack = function ( name, view y_center = (mode === "Dense" ? 1 : (1 + slots[feature_uid])) * y_scale; if (result.dataset_type === "bai") { + var cigar = feature[4]; ctx.fillStyle = block_color; - if (feature[4] instanceof Array) { - var b1_start = Math.floor( Math.max(0, (feature[4][0] - tile_low) * w_scale) ), - b1_end = Math.ceil( Math.min(width, Math.max(0, (feature[4][1] - tile_low) * w_scale)) ), - b2_start = Math.floor( Math.max(0, (feature[5][0] - tile_low) * w_scale) ), - b2_end = Math.ceil( Math.min(width, Math.max(0, (feature[5][1] - tile_low) * w_scale)) ); + if (feature[5] instanceof Array) { + var b1_start = Math.floor( Math.max(0, (feature[5][0] - tile_low) * w_scale) ), + b1_end = Math.ceil( Math.min(width, Math.max(0, (feature[5][1] - tile_low) * w_scale)) ), + b2_start = Math.floor( Math.max(0, (feature[6][0] - tile_low) * w_scale) ), + b2_end = Math.ceil( Math.min(width, Math.max(0, (feature[6][1] - tile_low) * w_scale)) ); - if (feature[4][1] >= tile_low && feature[4][0] <= tile_high) { - this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature[4][0], feature[4][2], b1_start + left_offset, b1_end - b1_start, y_center); + if (feature[5][1] >= tile_low && feature[5][0] <= tile_high) { + this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature[5][0], feature[5][2], b1_start + left_offset, b1_end - b1_start, y_center); } - if (feature[5][1] >= tile_low && feature[5][0] <= tile_high) { - this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature[5][0], feature[5][2], b2_start + left_offset, b2_end - b2_start, y_center); + if (feature[6][1] >= tile_low && feature[6][0] <= tile_high) { + this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature[6][0], feature[6][2], b2_start + left_offset, b2_end - b2_start, y_center); } if (b2_start > b1_end) { ctx.fillStyle = "#999"; --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -97,7 +97,7 @@ class SummaryTreeDataProvider( TracksDat resolution = max(1, ceil(float(kwargs['resolution']))) - level = ceil( log( resolution, st.block_size ) ) + level = ceil( log( resolution, st.block_size ) ) - 1 level = int(max( level, 0 )) if level <= 0: return None @@ -167,6 +167,7 @@ class BamDataProvider( TracksDataProvide Fetch intervals in the region """ start, end = int(start), int(end) + no_detail = "no_detail" in kwargs # Attempt to open the BAM file with index bamfile = csamtools.Samfile( filename=self.original_dataset.file_name, mode='rb', index_filename=self.converted_dataset.file_name ) message = None @@ -189,16 +190,20 @@ class BamDataProvider( TracksDataProvide message = "Only the first %s pairs are being displayed." % MAX_VALS break qname = read.qname + if no_detail: + seq = len(read.seq) + else: + seq = read.seq if read.is_proper_pair: if qname in paired_pending: # one in dict is always first pair = paired_pending[qname] - results.append( [ qname, pair['start'], read.pos + read.rlen, read.seq, [pair['start'], pair['end'], pair['seq']], [read.pos, read.pos + read.rlen, read.seq] ] ) + results.append( [ qname, pair['start'], read.pos + read.rlen, seq, read.cigar, [pair['start'], pair['end'], pair['seq']], [read.pos, read.pos + read.rlen, seq] ] ) # results.append( [read.qname, pair['start'], read.pos + read.rlen, qname, [pair['start'], pair['end']], [read.pos, read.pos + read.rlen] ] ) del paired_pending[qname] else: - paired_pending[qname] = { 'start': read.pos, 'end': read.pos + read.rlen, 'seq': read.seq, 'mate_start': read.mpos, 'rlen': read.rlen } + paired_pending[qname] = { 'start': read.pos, 'end': read.pos + read.rlen, 'seq': seq, 'mate_start': read.mpos, 'rlen': read.rlen, 'cigar': read.cigar } else: - results.append( [qname, read.pos, read.pos + read.rlen, read.seq] ) + results.append( [qname, read.pos, read.pos + read.rlen, seq, read.cigar] ) # take care of reads whose mates are out of range for qname, read in paired_pending.iteritems(): if read['mate_start'] < read['start']: @@ -212,7 +217,7 @@ class BamDataProvider( TracksDataProvide r1 = [read['start'], read['end'], read['seq']] r2 = [read['mate_start'], read['mate_start'] + read['rlen']] - results.append( [ qname, start, end, read['seq'], r1, r2 ] ) + results.append( [ qname, start, end, read['seq'], read['cigar'], r1, r2 ] ) bamfile.close() return { 'data': results, 'message': message } --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -6,7 +6,7 @@ .nav-controls a{padding:0 0.4em;} .nav-input{font-size:12px;width:30em;z-index:1000;} .location{display:inline-block;width:15em;margin:0px 10px;} -.draghandle{float:left;background:transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;width:10px;height:12px;margin-right:5px;} +.draghandle{cursor:move;float:left;background:transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;width:10px;height:12px;} .intro{z-index:1000;margin-left:auto;margin-right:auto;color:#555;text-align:center;font-size:16px;} .overview{width:100%;margin:0px;color:white;} .overview-viewport{position:relative;height:14px;background:white;border-bottom:solid gray 1px;margin:0;} @@ -18,11 +18,12 @@ .viewport-canvas{width:100%;height:100px;} .yaxislabel{color:#777;} .line-track .track-content{border-top:1px solid #ddd;border-bottom:1px solid #ddd;} -.track{background:white;} +.track{background:white;margin-bottom:1px;} .track-header{text-align:left;padding:4px 0px;color:#666;} +.track-header .menubutton{margin-left:3px;} .track-content{overflow:hidden;text-align:center;} -.track.error{margin-bottom:2px;background-color:#ECB4AF;} -.track.nodata{margin-bottom:2px;background-color:#ddd;} +.track.error{background-color:#ECB4AF;} +.track.nodata{background-color:#ddd;} .loading{min-height:100px;} .label-track{} .label-track .label{border-left:solid #999 1px;padding:1px;display:inline-block;} --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -35,11 +35,11 @@ margin: 0px 10px; } .draghandle { + cursor: move; float: left; background: transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat; width: 10px; height: 12px; - margin-right: 5px; } .intro { z-index: 1000; @@ -127,6 +127,7 @@ /* border-top: solid #DDDDDD 1px; */ /* border-bottom: solid #DDDDDD 1px; */ background: white; + margin-bottom: 1px; } .track-header { @@ -135,17 +136,19 @@ color: #666; } +.track-header .menubutton { + margin-left: 3px; +} + .track-content { overflow: hidden; text-align: center; } .track.error { - margin-bottom: 2px; background-color: #ECB4AF; } .track.nodata { - margin-bottom: 2px; background-color: #ddd; } --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function() {RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this. min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview -close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div />").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<inp ut/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(d){if(d.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=d.chrom_info ;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var d in a.tracks){a.tracks[d].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(d){this.origin al_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a.container.offset().left,h=(a.high-a. low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(c.chrom===""){c.intro_div.show()}else{c.intro_div.hide()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.reset();c.redraw(true);for(var g i n c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.overview_viewport.find("canvas").remove();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()} );delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=this.low/(this.max_high-this.max_low)*this.overview_viewport.width();var e=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width();var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,widt h:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()}});var Track=function(b,a,c){this.name=b;this.parent_element=c;this.view=a;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<div />").addClass("track");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this. container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name)}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Erro r","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var d=this,c=d.view;if(d.hidden){return}if(d.display_modes!==undefined){if(d.mode_div===undefined){d.mode_div=$("<div class='right-float menubutton popup' />").appendTo(d.header_div);var h=d.display_modes[0];d.mode=h;d.mode_div.text(h);var a=function(j){d.mode_div.text(j);d.mode=j;d.tile_cache.clear();d.draw()};var f={};for(var e in d.display_m odes){var g=d.display_modes[e];f[g]=function(j){return function(){a(j)}}(g)}make_popupmenu(d.mode_div,f)}else{d.mode_div.hide()}}var b={};b["Set as overview"]=function(){c.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var j in c.tracks){if(c.tracks[j]!==d){c.tracks[j].is_overview=false}}};b["Edit configuration"]=function(){var k=function(){hide_modal()};var j=function(){d.update_options(d.track_id);hide_modal()};show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:k,OK:j})};b.Remove=function(){c.remove_track(d);if(c.num_tracks===0){$("#no-tracks").show()}};make_popupmenu(d.name_div,b)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;var l=$("<div style='position: relative;'></div>"),m=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(l),this.max_height=0;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d) <e){var k=this.content_div.width()+"_"+m+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,k,j,e,a,d,l,m)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){if(!c.initial_canvas){c.initial_canvas=$(tile_element).clone();var l=tile_element.get(0).getContext("2d");var j=c.initial_canvas.get(0).getContext("2d");var k=l.getImageData(0,0,l.canvas.width,l.canvas.height);j.putImageData(k,0,0);c.set_overview()}c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)},set_overview:function(){var a=this.view;a.overview_viewport.height(a.default_overview_height);a.overview_box.h eight(a.default_overview_height);if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.trac k_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),n=e.get(0).getContext("2d"),j=f+"_"+b;if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m ===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o);n.fillText(m[h],a+this.left_offset,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Line","Filled","Intensity"];this.mode="Line";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefi ned;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();a.container_div.css("position","relative");var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);e.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});e.prependTo(a.cont ainer_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();if(data.length>1){var f=M ath.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(k){var a=$("<div />").addClass("form-row");var e="track_"+k+"_minval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),j=$("<input></input>").attr("id",e).val(b),g="track_"+k+"_maxval",d=$("<label></label>").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs .max_value),c=$("<input></input>").attr("id",g).val(f);return a.append(h).append(j).append(d).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=20;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"black",label_color:"black",show_counts:true};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_ca che.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y [0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(ae,o,r,ar){var L=o*DENSITY*ae,ak=(o+1)*DENSITY*ae,K=ak-L;var al=(!this.initial_canvas?"initial":L+"_"+ak);var G=this.data_cache.get(al);var e;if(G===undefined||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ak]]=true;this.get_data(L,ak);return}var a=Math.ceil(K*ar),S=$("<canvas class='tile'></canvas>"),ag=this.pr efs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ac=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),W=this.left_offset,aq,B,at;if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ac?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/view.zoom_res:ar);B=this.incremental_slots(w,G.data,ac,q)*at+v;aq=this.inc_slots[w]}}S.css({position:"absolute",top:0,left:(L-this.view.low)*ar-W});S.get(0).width=a+W;S.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=S.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";if(G.dataset_type=="summary_tree"){var R,O=55,aj=255-O,n=aj*2/3,Y=G.data,J=G.max,p=G.avg,b=Math.ceil(G.delta*ar);for(var an=0,F=Y.length;an<F;an++){var aa=Math.floor((Y[an][0]-L)*ar);var Z=Y[an][1];if(!Z){continue}R=Math.floor(aj-(Z/J)*aj);H.fillStyle="rgb("+R+","+R+","+R+")";H.fillRect(aa+W,0,b,this.su mmary_draw_height);if(this.prefs.show_counts&&H.measureText(Z).width<b){if(R>n){H.fillStyle="black"}else{H.fillStyle="#ddd"}H.textAlign="center";H.fillText(Z,aa+W+(b/2),12)}}e="Summary";r.append(S);return S}if(G.message){S.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+W,at)}var ap=G.data;var am=0;for(var an=0,F=ap.length;an<F;an++){var T=ap[an],Q=T[0],ao=T[1],ab=T[2],M=T[3];if(ao<=ak&&ab>=L){var ad=Math.floor(Math.max(0,(ao-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(ab-L)*ar))),X=(q==="Dense"?1:(1+aq[Q]))*at;if(G.dataset_type==="bai"){H.fillStyle=h;if(T[4] instanceof Array){var C=Math.floor(Math.max(0,(T[4][0]-L)*ar)),P=Math.ceil(Math.min(a,Math.max(0,(T[4][1]-L)*ar))),A=Math.floor(Math.max(0,(T[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(T[5][1]-L)*ar)));if(T[4][1]>=L&&T[4][0]<=ak){this.rect_or_text(H,ar,L,ak,T[4][0],T[4][2],C+W,P-C,X)}if(T[5][1]>=L&&T[5][0]<=ak){this.rect_or_text(H,ar,L,ak,T[5] [0],T[5][2],A+W,u-A,X)}if(A>P){H.fillStyle="#999";H.fillRect(P+W,X+5,A-P,1)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ak,ao,M,ad+W,I-ad,X)}if(q!=="Dense"&&!ac&&ao>L){H.fillStyle=this.prefs.label_color;if(o===0&&ad-H.measureText(M).width<0){H.textAlign="left";H.fillText(Q,I+2+W,X+8)}else{H.textAlign="right";H.fillText(Q,ad-2+W,X+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ac){H.fillStyle=h;H.fillRect(ad+W,X+5,I-ad,1)}else{var E=T[4],V=T[5],af=T[6],g=T[7];var D,ah,N=null,au=null;if(V&&af){N=Math.floor(Math.max(0,(V-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(af-L)*ar)))}if(q!=="Dense"&&M!==undefined&&ao>L){H.fillStyle=ag;if(o===0&&ad-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+W,X+8)}else{H.textAlign="right";H.fillText(M,ad-2+W,X+8)}H.fillStyle=h}if(g){if(E){if(E=="+"){H.fillStyle=RIGHT_STRAND}else{if(E=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ad+W,X,I-ad,10);H.fillStyle=h}for(var al=0,f=g.length;al<f;al++){var t=g[al],d=Math.floor(Mat h.max(0,(t[0]-L)*ar)),U=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>U){continue}D=5;ah=3;H.fillRect(d+W,X+ah,U-d,D);if(N!==undefined&&!(d>au||U<N)){D=9;ah=1;var ai=Math.max(d,N),z=Math.min(U,au);H.fillRect(ai+W,X+ah,z-ai,D)}}}else{D=9;ah=1;H.fillRect(ad+W,X+ah,I-ad,D);if(T.strand){if(T.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(T.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ad+W,X,I-ad,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ac){H.fillStyle=h;H.fillRect(ad+W,X+5,I-ad,1)}else{var s=T[4],m=T[5],c=T[6];D=9;ah=1;H.fillRect(ad+W,X,I-ad,D);if(q!=="Dense"&&M!==undefined&&ao>L){H.fillStyle=ag;if(o===0&&ad-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+W,X+8)}else{H.textAlign="right";H.fillText(M,ad-2+W,X+8)}H.fillStyle=h}var l=s+" / "+m;if(ao>L&&H.measureText(l).width<(I-ad)){H.fillStyle="white";H.textAlign="center";H.fillText(l,W+ad+(I-ad)/2,X+8);H.fillStyle=h}}}}}am++}}r.append(S);return S},gen_options:function(j){var a=$("<div / >").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs .show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c){FeatureTrack.call(this,d,b,a,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); +var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function() {RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this. min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview -close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div />").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<inp ut/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(d){if(d.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=d.chrom_info ;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var d in a.tracks){a.tracks[d].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(d){this.origin al_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a.container.offset().left,h=(a.high-a. low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(c.chrom===""){c.intro_div.show()}else{c.intro_div.hide()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.reset();c.redraw(true);for(var g i n c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.reset_overview();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this .tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=this.low/(this.max_high-this.max_low)*this.overview_viewport.width();var e=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width();var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_locatio n(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Track=function(b,a,c){this.name=b;this.parent_ element=c;this.view=a;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<div />").addClass("track");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name)}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(D ATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var d=this,c=d.view;if(d.hidden){return}if(d.display_modes!==undefined){if(d.mode_div===undefined){d.mode_div=$("<div class= 'right-float menubutton popup' />").appendTo(d.header_div);var h=d.display_modes[0];d.mode=h;d.mode_div.text(h);var a=function(j){d.mode_div.text(j);d.mode=j;d.tile_cache.clear();d.draw()};var f={};for(var e in d.display_modes){var g=d.display_modes[e];f[g]=function(j){return function(){a(j)}}(g)}make_popupmenu(d.mode_div,f)}else{d.mode_div.hide()}}var b={};b["Set as overview"]=function(){c.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var j in c.tracks){if(c.tracks[j]!==d){c.tracks[j].is_overview=false}}};b["Edit configuration"]=function(){var k=function(){hide_modal()};var j=function(){d.update_options(d.track_id);hide_modal()};show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:k,OK:j})};b.Remove=function(){c.remove_track(d);if(c.num_tracks===0){$("#no-tracks").show()}};make_popupmenu(d.name_div,b)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution ;var l=$("<div style='position: relative;'></div>"),m=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(l),this.max_height=0;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+m+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,k,j,e,a,d,l,m)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){if(!c.initial_canvas){c.initial_canvas=$(tile_element).clone();var l=tile_element.get(0).getContext("2d");var j=c.initial_canvas.get(0).getContext("2d");var k=l.getImageData(0,0,l.canvas.width,l.canvas.height);j.putImageData(k,0,0);c.set_overview()}c.tile_cache.set(e,tile_element); c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a +=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,l,p){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),o=e.get(0).get Context("2d"),k=f+"_"+b;if(p>PX_PER_CHAR){if(this.data_cache.get(k)===undefined){this.get_data(f,b);return}var n=this.data_cache.get(k);if(n===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*p+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*p-this.left_offset});for(var h=0,m=n.length;h<m;h++){var a=Math.round(h*p),j=Math.round(p/2);o.fillText(n[h],a+this.left_offset+j,10)}l.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Line","Filled","Intensity"];this.mode="Line";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){thi s.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();a.container_div.css("position","relative");var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.cs s({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);e.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false ,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(k){var a=$("<div />").addClass("form-row");var e="track_"+k+"_minval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),j=$("<input ></input>").attr("id",e).val(b),g="track_"+k+"_maxval",d=$("<label></label>").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs.max_value),c=$("<input></input>").attr("id",g).val(f);return a.append(h).append(j).append(d).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show _labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"black",label_color:"black",show_counts:true};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data _queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}v ar v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(ac,n,q,ap){var L=n*DENSITY*ac,ah=(n+1)*DENSITY*ac,K=ah-L;var aj=(!this.initial_canvas?"initial":L+"_"+ah);var G=this.data_cache.get(aj);var e;if(G===undefined||(this.mode!=="Auto"&& G.dataset_type==="summary_tree")){this.data_queue[[L,ah]]=true;this.get_data(L,ah);return}var a=Math.ceil(K*ap),Q=$("<canvas class='tile'></canvas>"),ae=this.prefs.label_color,h=this.prefs.block_color,p=this.mode,v=25,aa=(p==="Squish")||(p==="Dense")&&(p!=="Pack")||(p==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,ao,B,aq;if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(p==="Dense"){B=v;aq=10}else{aq=(aa?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ap<0.0001?1/view.zoom_res:ap);B=this.incremental_slots(w,G.data,aa,p)*aq+v;ao=this.inc_slots[w]}}Q.css({position:"absolute",top:0,left:(L-this.view.low)*ap-U});Q.get(0).width=a+U;Q.get(0).height=B;q.parent().css("height",Math.max(this.height_px,B)+"px");var H=Q.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,o=G.avg,b=Math.ceil(G.delta*ap);for(var al=0,F=W.length;al<F;al++){var Y=Math.floor((W[a l][0]-L)*ap);var X=W[al][1];if(!X){continue}var ai=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-ai,b,ai);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}e="Summary";q.append(Q);return Q}if(G.message){Q.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,aq)}var an=G.data;var ak=0;for(var al=0,F=an.length;al<F;al++){var R=an[al],P=R[0],am=R[1],Z=R[2],M=R[3];if(am<=ah&&Z>=L){var ab=Math.floor(Math.max(0,(am-L)*ap)),I=Math.ceil(Math.min(a,Math.max(0,(Z-L)*ap))),V=(p==="Dense"?1:(1+ao[P]))*aq;if(G.dataset_type==="bai"){var t=R[4];H.fillStyle=h;if(R[5] instanceof Array){var C=Math.floor(Math.max(0,(R[5][0]-L)*ap)),O=Math.ceil(Math.min(a,Math.max(0,(R[5][1]-L)*ap))),A=Math.floor(Math.max(0,(R[6][0]-L)*ap)),u=Math.ceil(Math.min(a,Math.max(0,(R[6][1]-L)*ap)));if(R[5][1]>=L&& R[5][0]<=ah){this.rect_or_text(H,ap,L,ah,R[5][0],R[5][2],C+U,O-C,V)}if(R[6][1]>=L&&R[6][0]<=ah){this.rect_or_text(H,ap,L,ah,R[6][0],R[6][2],A+U,u-A,V)}if(A>O){H.fillStyle="#999";H.fillRect(O+U,V+5,A-O,1)}}else{H.fillStyle=h;this.rect_or_text(H,ap,L,ah,am,M,ab+U,I-ab,V)}if(p!=="Dense"&&!aa&&am>L){H.fillStyle=this.prefs.label_color;if(n===0&&ab-H.measureText(M).width<0){H.textAlign="left";H.fillText(P,I+2+U,V+8)}else{H.textAlign="right";H.fillText(P,ab-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(aa){H.fillStyle=h;H.fillRect(ab+U,V+5,I-ab,1)}else{var E=R[4],T=R[5],ad=R[6],g=R[7];var D,af,N=null,ar=null;if(T&&ad){N=Math.floor(Math.max(0,(T-L)*ap));ar=Math.ceil(Math.min(a,Math.max(0,(ad-L)*ap)))}if(p!=="Dense"&&M!==undefined&&am>L){H.fillStyle=ae;if(n===0&&ab-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ab-2+U,V+8)}H.fillStyle=h}if(g){if(E){if(E=="+"){H.fillStyle=RIGHT_STRAND}else{if(E=="-"){H 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n="center";H.fillText(l,U+ab+(I-ab)/2,V+8);H.fillStyle=h}}}}}ak++}}q.append(Q);return Q},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.b lock_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c){FeatureTrack.call(this,d,b,a,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});

1 0

galaxy-dist commit d8da4f7bb0f5: Add -ungapped for blastn and blastx (having trouble with blastp and tblastn, not in tblastx)
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 1286554738 -3600 # Node ID d8da4f7bb0f5e1d43b371e4e52fb688ad816e5bf # Parent 8979b429d7691f4121afb368a05e6b9d0ea40706 Add -ungapped for blastn and blastx (having trouble with blastp and tblastn, not in tblastx) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -25,6 +25,7 @@ blastn #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): -word_size $adv_opts.word_size #end if +$adv_opts.ungapped </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -76,6 +77,7 @@ blastn <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="advanced"> @@ -93,6 +95,7 @@ blastn <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4."><validator type="in_range" min="0" /></param> + <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -25,6 +25,8 @@ blastp #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): -word_size $adv_opts.word_size #end if +##Ungapped disabled for now - see comments below +##$adv_opts.ungapped </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> @@ -70,6 +72,10 @@ blastp <param name="matrix" type="hidden" value="" /><param name="max_hits" type="hidden" value="" /><param name="word_size" type="hidden" value="" /> + </when><when value="advanced"> @@ -92,6 +98,12 @@ blastp <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."><validator type="in_range" min="0" /></param> + </when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -25,6 +25,7 @@ blastx #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): -word_size $adv_opts.word_size #end if +$adv_opts.ungapped </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -67,6 +68,7 @@ blastx <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="advanced"> @@ -94,6 +96,7 @@ blastx <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."><validator type="in_range" min="0" /></param> + <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -24,6 +24,8 @@ tblastn #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): -word_size $adv_opts.word_size #end if +##Ungapped disabled for now - see comments below +##$adv_opts.ungapped </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> @@ -65,6 +67,10 @@ tblastn <param name="matrix" type="hidden" value="" /><param name="max_hits" type="hidden" value="" /><param name="word_size" type="hidden" value="" /> + </when><when value="advanced"> @@ -87,6 +93,12 @@ tblastn <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."><validator type="in_range" min="0" /></param> + </when></conditional></inputs>

1 0

galaxy-dist commit 4d5b00b6fe74: Show Image type datasets inline in browser
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 1287007951 14400 # Node ID 4d5b00b6fe741a35320a572302d1fb8bb7eb6971 # Parent 5f4ad373807158f8b2ac0bcaafab9f57b972e562 Show Image type datasets inline in browser --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -350,7 +350,7 @@ class DatasetInterface( BaseController, trans.response.set_content_type(mime) trans.log_event( "Display dataset id: %s" % str( dataset_id ) ) - if to_ext or isinstance(data.datatype, datatypes.binary.Binary) or isinstance(data.datatype, datatypes.images.Image): # Saving the file, or binary/image file + if to_ext or isinstance(data.datatype, datatypes.binary.Binary): # Saving the file, or binary file if data.extension in composite_extensions: return self.archive_composite_dataset( trans, data, **kwd ) else: @@ -366,13 +366,13 @@ class DatasetInterface( BaseController, raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % data.file_name ) max_peek_size = 1000000 # 1 MB - if preview and os.stat( data.file_name ).st_size > max_peek_size: + if not preview or isinstance(data.datatype, datatypes.images.Image) or os.stat( data.file_name ).st_size < max_peek_size: + return open( data.file_name ) + else: trans.response.set_content_type( "text/html" ) return trans.stream_template_mako( "/dataset/large_file.mako", truncated_data = open( data.file_name ).read(max_peek_size), data = data ) - else: - return open( data.file_name ) @web.expose @web.require_login( "see all available datasets" )

1 0

galaxy-dist commit 76f09e5ccb85: sample tracking UI fixes
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1287002139 14400 # Node ID 76f09e5ccb85569b56e66676e4c761f4348336fc # Parent c0feb970e48de8b713a9a516cad61950ed0641b5 sample tracking UI fixes --- a/templates/requests/common/manage_request.mako +++ b/templates/requests/common/manage_request.mako @@ -132,38 +132,38 @@ <div class="grid-header"><h2>Sequencing Request "${request.name}"</h2> + + <ul class="manage-table-actions"> + <li><a class="action-button" id="seqreq-${request.id}-popup" class="menubutton">Sequencing Request Actions</a></li> + <div popupmenu="seqreq-${request.id}-popup"> + %if request.is_unsubmitted and request.samples: + <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit</a> + %endif + <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">History</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit</a> + %if is_admin: + %if request.is_submitted: + <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> + %endif + %endif + </div> + <li><a class="action-button" href="${h.url_for( controller=cntrller, action='browse_requests' )}">Browse requests</a></li> + </ul> + <div class="toolParamHelp" style="clear: both;"> - <b>Sequencer</b>: ${request.type.name} - %if is_admin: - | <b>User</b>: ${request.user.email} - %endif - %if request.is_submitted: - | <b>State</b>: <i>${request.state}</i> - %else: - | <b>State</b>: ${request.state} - %endif + <b>Sequencer</b>: ${request.type.name} + %if is_admin: + | <b>User</b>: ${request.user.email} + %endif + %if request.is_submitted: + | <b>State</b>: <i>${request.state}</i> + %else: + | <b>State</b>: ${request.state} + %endif </div></div> -<br/><br/> -<ul class="manage-table-actions"> - <li><a class="action-button" id="seqreq-${request.id}-popup" class="menubutton">Sequencing Request Actions</a></li> - <div popupmenu="seqreq-${request.id}-popup"> - %if request.is_unsubmitted and request.samples: - <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit</a> - %endif - <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">History</a> - <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit</a> - %if is_admin: - %if request.is_submitted: - <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> - <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> - %endif - %endif - </div> - <li><a class="action-button" href="${h.url_for( controller=cntrller, action='browse_requests' )}">Browse requests</a></li> -</ul> - %if request.has_samples_without_library_destinations: ${render_msg( "Select a target data library and folder for all the samples before starting the sequence run", "warning" )} %endif --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -393,7 +393,8 @@ class RequestsAdmin( BaseController, Use # get the sample these datasets are associated with try: sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( selected_sample_id ) ) - sample.library.id and sample.folder.id + if sample.name in sample.request.has_samples_without_library_destinations: + raise Exception() except: # if no sample (with associated library & folder) has been selected status = 'error'

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galaxy-dist commit c0feb970e48d: sample tracking bug fixes
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1287000426 14400 # Node ID c0feb970e48de8b713a9a516cad61950ed0641b5 # Parent 77e13329ab8b9e69089400259eb70cda9525ec80 sample tracking bug fixes --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -3,15 +3,14 @@ <% from galaxy.web.controllers.requests_admin import build_rename_datasets_for_sample_select_field %> -<br/><br/> -<font color="red"><b><i>A dataset can be renamed only if its status is "Not Started"</i></b></font> +<h3>Rename datasets for Sample "${sample.name}"</h3><ul class="manage-table-actions"><li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Browse datasets</a></li><li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller='requests_admin', id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li></ul> @@ -19,40 +18,39 @@ ${render_msg( message, status )} %endif +${render_msg( 'A dataset can be renamed only if it is in <b>Not Started</b> state.', 'warning' )} <div class="toolForm"> - <div class="toolFormTitle">Rename datasets for Sample "${sample.name}"</div> - <div class="toolFormBody"> - <form name="rename_datasets" id="rename_datasets" action="${h.url_for( controller='requests_admin', action='rename_datasets', id_list=id_list, sample_id=trans.security.encode_id( sample.id ) )}" method="post" > - <table class="grid"> - <thead> - <tr> - <th>Prepend directory name</th> - <th>Name</th> - <th>Path on sequencer</th> - </tr> - <thead> - <tbody> - %for sample_dataset in sample_datasets: - %if sample_dataset.status == trans.app.model.Sample.transfer_status.NOT_STARTED: - <tr> - <td> - <% rename_datasets_for_sample_select_field = build_rename_datasets_for_sample_select_field( trans, sample_dataset ) %> - ${rename_datasets_for_sample_select_field} - </td> - <td> - <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id} )" value="${sample_dataset.name}" size="100"/> - </td> - <td>${sample_dataset.file_path}</td> - </tr> - %endif - %endfor - </tbody> - </table> - <br/> - <div class="form-row"> - <input type="submit" name="rename_datasets_button" value="Save"/> - <input type="submit" name="cancel_rename_datasets_button" value="Close"/> - </div> - </form> - </div> + <form name="rename_datasets" id="rename_datasets" action="${h.url_for( controller='requests_admin', action='rename_datasets', id_list=id_list, sample_id=trans.security.encode_id( sample.id ) )}" method="post" > + <table class="grid"> + <thead> + <tr> + <th>Prepend directory name</th> + <th>Name</th> + <th>Path on sequencer</th> + </tr> + <thead> + <tbody> + %for id in id_list: + <% sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( id ) ) %> + %if sample_dataset.status == trans.app.model.Sample.transfer_status.NOT_STARTED: + <tr> + <td> + <% rename_datasets_for_sample_select_field = build_rename_datasets_for_sample_select_field( trans, sample_dataset ) %> + ${rename_datasets_for_sample_select_field.get_html()} + </td> + <td> + <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id ) }" value="${sample_dataset.name}" size="100"/> + </td> + <td>${sample_dataset.file_path}</td> + </tr> + %endif + %endfor + </tbody> + </table> + <br/> + <div class="form-row"> + <input type="submit" name="rename_datasets_button" value="Save"/> + <input type="submit" name="cancel_rename_datasets_button" value="Close"/> + </div> + </form></div> --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -105,8 +105,7 @@ class RequestsGrid( grids.Grid ): class RequestsCommon( BaseController, UsesFormDefinitionWidgets ): @web.json - def sample_state_updates( self, trans, ids=None, states=None, cntrller=None ): - # TODO fix this mthod - cntrller is required in the signature. + def sample_state_updates( self, trans, cntrller, ids=None, states=None ): # Avoid caching trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' @@ -424,13 +423,19 @@ class RequestsCommon( BaseController, Us except: invalid_id_redirect( trans, cntrller, folder_id ) for sample_id in selected_samples: - sample = trans.sa_session.query( trans.model.Sample ).get( sample_id ) + sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) sample.library = library sample.folder = folder trans.sa_session.add( sample ) trans.sa_session.flush() trans.sa_session.refresh( request ) message = 'Changes made to the selected samples have been saved. ' + return trans.response.send_redirect( web.url_for( controller='requests_common', + action='manage_request', + cntrller=cntrller, + id=request_id, + status=status, + message=message ) ) elif params.get( 'cancel_change_lib_button', False ): return trans.response.send_redirect( web.url_for( controller='requests_common', action='manage_request', @@ -859,7 +864,7 @@ class RequestsCommon( BaseController, Us # The user has selected a sample to copy. library_id = current_samples[ copy_sample_index][ 'library_select_field' ].get_selected( return_value=True ) folder_id = current_samples[ copy_sample_index ][ 'folder_select_field' ].get_selected( return_value=True ) - name = current_samples[ copy_sample_index ][ 'name' ] + '_%i' % ( index+1 ) + name = current_samples[ copy_sample_index ][ 'name' ] + '_%i' % ( len( current_samples ) + 1 ) library_id = 'none' folder_id = 'none' field_values = [ val for val in current_samples[ copy_sample_index ][ 'field_values' ] ] @@ -867,7 +872,7 @@ class RequestsCommon( BaseController, Us # The user has not selected a sample to copy (may just be adding a sample). library_id = None folder_id = None - name = 'Sample_%i' % ( sample_index+1 ) + name = 'Sample_%i' % ( len( current_samples ) + 1 ) field_values = [ '' for field in request.type.sample_form.fields ] # Build the library_select_field and folder_select_field for the new sample being added. library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans, --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -9,11 +9,13 @@ import logging, os, pexpect, ConfigParse log = logging.getLogger( __name__ ) -class UserColumn( grids.TextColumn ): - def get_value( self, trans, grid, request ): - return request.user.email + class AdminRequestsGrid( RequestsGrid ): + class UserColumn( grids.TextColumn ): + def get_value( self, trans, grid, request ): + return request.user.email + # Grid definition columns = [ col for col in RequestsGrid.columns ] columns.append( UserColumn( "User", model_class=model.User, @@ -180,7 +182,7 @@ class RequestsAdmin( BaseController, Use @web.json def get_file_details( self, trans, id, folder_path ): def print_ticks( d ): - # TODO: why is this method here? Add comments! + # pexpect timeout method pass # Avoid caching trans.response.headers['Pragma'] = 'no-cache' @@ -243,16 +245,20 @@ class RequestsAdmin( BaseController, Use if not sample_dataset_id: return invalid_id_redirect( trans, 'requests_admin', sample_dataset_id ) id_list = util.listify( sample_dataset_id ) + selected_sample_datasets = [] + for sample_dataset_id in id_list: + try: + selected_sample_datasets.append( trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) ) + except: + return invalid_id_redirect( trans, 'requests_admin', sample_dataset_id ) if operation == "view": - sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) return trans.fill_template( '/admin/requests/dataset.mako', - sample_dataset=sample_dataset ) + sample_dataset=selected_sample_datasets[0] ) elif operation == "delete": not_deleted = [] - for sample_dataset_id in id_list: - sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) - sample_id = sample_dataset.sample_id - if sample_dataset.status == sample_dataset.sample.transfer_status.NOT_STARTED: + for sample_dataset in selected_sample_datasets: + sample_id = sample_dataset.sample.id + if sample_dataset.status == trans.app.model.Sample.transfer_status.NOT_STARTED: trans.sa_session.delete( sample_dataset ) trans.sa_session.flush() else: @@ -267,13 +273,26 @@ class RequestsAdmin( BaseController, Use status=status, message=message ) ) elif operation == "rename": - sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) + # if none of the selected sample datasets are in the NOT_STARTED state, + # then display error message + flag = True + for sd in selected_sample_datasets: + if sd.status == trans.app.model.Sample.transfer_status.NOT_STARTED: + flag = False + break + if flag: + status = 'error' + message = 'A dataset can be renamed only if it is in the <b>Not Started</b> state.' + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='manage_datasets', + sample_id=trans.security.encode_id( selected_sample_datasets[0].sample.id ), + status=status, + message=message ) ) return trans.fill_template( '/admin/requests/rename_datasets.mako', - sample=sample_dataset.sample, + sample=selected_sample_datasets[0].sample, id_list=id_list ) elif operation == "start transfer": - sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) - self.__start_datatx( trans, sample_dataset.sample, id_list ) + self.__start_datatx( trans, selected_sample_datasets[0].sample, selected_sample_datasets ) # Render the grid view sample_id = params.get( 'sample_id', None ) try: @@ -340,7 +359,7 @@ class RequestsAdmin( BaseController, Use message = 'Changes saved successfully.' return trans.fill_template( '/admin/requests/rename_datasets.mako', sample=sample, - sample_datasets=sample_datasets, + id_list=id_list, message=message, status=status ) return trans.response.send_redirect( web.url_for( controller='requests_admin', @@ -353,38 +372,48 @@ class RequestsAdmin( BaseController, Use message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) request_id = kwd.get( 'request_id', None ) + files = [] try: request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) except: return invalid_id_redirect( trans, 'requests_admin', request_id ) - files_list = util.listify( params.get( 'files_list', [] ) ) + selected_files = util.listify( params.get( 'files_list', [] ) ) folder_path = util.restore_text( params.get( 'folder_path', request.type.datatx_info[ 'data_dir' ] ) ) - selected_value = kwd.get( 'sample_id', 'none' ) - sample_id_select_field = self.__build_sample_id_select_field( request, selected_value ) + selected_sample_id = kwd.get( 'sample_id', 'none' ) + sample_id_select_field = self.__build_sample_id_select_field( trans, request, selected_sample_id ) # The __get_files() method redirects here with a status of 'error' and a message if there # was a problem retrieving the files. if folder_path and status != 'error': folder_path = self.__check_path( folder_path ) - sample_id = params.get( 'sample_id', None ) - try: - sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) - except: - return invalid_id_redirect( trans, 'requests_admin', sample_id ) - # Get the filenames from the remote host - files = self.__get_files( trans, request, folder_path ) - if params.get( 'open_folder', False ): - if len( files_list ) == 1: - folder_path = os.path.join( folder_path, files_list[0] ) - folder_path = self.__check_path( folder_path ) + if params.get( 'folder_up', False ): + if folder_path[-1] == os.sep: + folder_path = os.path.dirname(folder_path[:-1]) + folder_path = self.__check_path( folder_path ) elif params.get( 'select_show_datasets_button', False ) or params.get( 'select_more_button', False ): - sample_dataset_file_names = self.__save_sample_datasets( trans, sample, files_list, folder_path ) + # get the sample these datasets are associated with + try: + sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( selected_sample_id ) ) + sample.library.id and sample.folder.id + except: + # if no sample (with associated library & folder) has been selected + status = 'error' + message = 'Select a sample with associated data library and folder before selecting the dataset(s).' + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='get_data', + request_id=trans.security.encode_id( request.id ), + folder_path=folder_path, + status=status, + message=message ) ) + # save the sample datasets + sample_dataset_file_names = self.__save_sample_datasets( trans, sample, selected_files, folder_path ) if sample_dataset_file_names: message = 'Datasets (%s) have been selected for sample (%s)' % \ ( str( sample_dataset_file_names )[1:-1].replace( "'", "" ), sample.name ) if params.get( 'select_show_datasets_button', False ): return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_datasets', - sample_id=sample_id, + request_id=request_id, + sample_id=trans.security.encode_id( sample.id ), message=message, status=status ) ) else: # 'select_more_button' was clicked @@ -392,11 +421,13 @@ class RequestsAdmin( BaseController, Use action='get_data', request_id=request_id, folder_path=folder_path, - sample_id=sample_id, + sample_id=sample.id, open_folder=True, message=message, status=status ) ) - return trans.fill_template( '/admin/requests/dataset_transfer.mako', + # Get the filenames from the remote host + files = self.__get_files( trans, request, folder_path ) + return trans.fill_template( '/admin/requests/get_data.mako', cntrller='requests_admin', request=request, sample_id_select_field=sample_id_select_field, @@ -434,20 +465,20 @@ class RequestsAdmin( BaseController, Use if ok: return output.splitlines() return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='get_data', - request_id=trans.security.encode_id( request.id ), - folder_path=folder_path, - status=status, - message=message ) ) + action='get_data', + request_id=trans.security.encode_id( request.id ), + folder_path=folder_path, + status=status, + message=message ) ) def __check_path( self, a_path ): # Return a valid folder_path if a_path and not a_path.endswith( os.sep ): a_path += os.sep return a_path - def __save_sample_datasets( self, trans, sample, files_list, folder_path ): + def __save_sample_datasets( self, trans, sample, selected_files, folder_path ): sample_dataset_file_names = [] - if files_list: - for f in files_list: + if selected_files: + for f in selected_files: filepath = os.path.join( folder_path, f ) if f[-1] == os.sep: # FIXME: The selected item is a folder so transfer all the folder contents @@ -522,7 +553,7 @@ class RequestsAdmin( BaseController, Use trans.sa_session.add( lfp ) trans.sa_session.flush() return datatx_user - def __send_message( self, trans, datatx_info, sample, id_list ): + def __send_message( self, trans, datatx_info, sample, selected_sample_datasets ): """Ceates an xml message and sends it to the rabbitmq server""" # Create the xml message based on the following template xml = \ @@ -542,8 +573,7 @@ class RequestsAdmin( BaseController, Use <file>%(FILE)s</file></dataset>''' datasets = '' - for id in id_list: - sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( id ) ) + for sample_dataset in selected_sample_datasets: if sample_dataset.status == sample.transfer_status.NOT_STARTED: datasets = datasets + dataset_xml % dict( ID=str( sample_dataset.id ), NAME=sample_dataset.name, @@ -574,7 +604,7 @@ class RequestsAdmin( BaseController, Use routing_key=trans.app.config.amqp['routing_key'] ) chan.close() conn.close() - def __start_datatx( self, trans, sample, id_list ): + def __start_datatx( self, trans, sample, selected_sample_datasets ): datatx_user = self.__setup_datatx_user( trans, sample.library, sample.folder ) # Validate sequencer information datatx_info = sample.request.type.datatx_info @@ -582,8 +612,8 @@ class RequestsAdmin( BaseController, Use message = "Error in sequencer login information." status = "error" else: - self.__send_message( trans, datatx_info, sample, id_list ) - message = "%i datasets have been queued for transfer from the sequencer. Click the Refresh button above to see the latest transfer status." % len( id_list ) + self.__send_message( trans, datatx_info, sample, selected_sample_datasets ) + message = "%i datasets have been queued for transfer from the sequencer. Click the Refresh button above to see the latest transfer status." % len( selected_sample_datasets ) status = "done" return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_datasets', @@ -599,6 +629,14 @@ class RequestsAdmin( BaseController, Use obj_id = kwd.get( 'id', None ) if operation == "view_form_definition": return self.view_form_definition( trans, **kwd ) + elif operation == "view": + return self.view_request_type( trans, **kwd ) + elif operation == "delete": + return self.delete_request_type( trans, **kwd ) + elif operation == "undelete": + return self.undelete_request_type( trans, **kwd ) + elif operation == "permissions": + return self.request_type_permissions( trans, **kwd ) # Render the grid view return self.requesttype_grid( trans, **kwd ) @web.expose @@ -655,26 +693,26 @@ class RequestsAdmin( BaseController, Use message=message, status=status ) def __create_request_type_form( self, trans, **kwd ): - request_form_definitionss = self.get_all_forms( trans, + request_form_definitions = self.get_all_forms( trans, filter=dict( deleted=False ), form_type=trans.model.FormDefinition.types.REQUEST ) sample_form_definitions = self.get_all_forms( trans, filter=dict( deleted=False ), form_type=trans.model.FormDefinition.types.SAMPLE ) - if not request_form_definitionss or not sample_form_definitions: + if not request_form_definitions or not sample_form_definitions: return [],[] params = util.Params( kwd ) request_form_id = params.get( 'request_form_id', 'none' ) sample_form_id = params.get( 'sample_form_id', 'none' ) request_form_id_select_field = build_select_field( trans, - objs=request_form_definitionss, - label_attr='id', + objs=request_form_definitions, + label_attr='name', select_field_name='request_form_id', selected_value=request_form_id, refresh_on_change=False ) sample_form_id_select_field = build_select_field( trans, objs=sample_form_definitions, - label_attr='id', + label_attr='name', select_field_name='sample_form_id', selected_value=sample_form_id, refresh_on_change=False ) @@ -826,7 +864,7 @@ class RequestsAdmin( BaseController, Use status=status, message=message ) # ===== Methods for building SelectFields used on various admin_requests forms - def __build_sample_id_select_field( self, request, selected_value ): + def __build_sample_id_select_field( self, trans, request, selected_value ): return build_select_field( trans, request.samples, 'name', 'sample_id', selected_value=selected_value, refresh_on_change=False ) def __build_rename_dataset_select_field( self, trans, request_type=None ): if request_type: --- a/templates/admin/requests/get_data.mako +++ b/templates/admin/requests/get_data.mako @@ -68,13 +68,6 @@ } </script> -<style type="text/css"> -.msg_head { - padding: 0px 0px; - cursor: pointer; -} -</style> - <br/><br/><ul class="manage-table-actions"> @@ -92,7 +85,7 @@ <div class="toolForm"><div class="toolFormTitle">Select files for transfer</div> - <form name="get_data" id="get_data" action="${h.url_for( controller='requests_admin', action='get_data', cntrller=cntrller, request_id=trans.security.encode_id( request.id )}" method="post" > + <form name="get_data" id="get_data" action="${h.url_for( controller='requests_admin', action='get_data', cntrller=cntrller, request_id=trans.security.encode_id( request.id ))}" method="post" ><div class="form-row"><label>Sample:</label> ${sample_id_select_field.get_html()} --- a/templates/requests/common/manage_request.mako +++ b/templates/requests/common/manage_request.mako @@ -62,7 +62,7 @@ // Build request data var ids = [] var states = [] - $.each( sample_states, function ( id, state ) { + $.each( sample_states, function ( id, state, cntrller ) { ids.push( id ); states.push( state ); }); @@ -73,7 +73,7 @@ dataType: "json", data: { ids: ids.join( "," ), states: states.join( "," ) }, success : function ( data ) { - $.each( data, function(id, val, cntrller ) { + $.each( data, function( cntrller, id, val ) { // Replace HTML var cell1 = $("#sampleState-" + id); cell1.html( val.html_state ); @@ -146,8 +146,6 @@ </div><br/><br/> -<font color="red"><b><i>A dataset can be renamed only if its status is "Not Started"</i></b></font> - <ul class="manage-table-actions"><li><a class="action-button" id="seqreq-${request.id}-popup" class="menubutton">Sequencing Request Actions</a></li><div popupmenu="seqreq-${request.id}-popup">

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galaxy-dist commit c8173a50bc9b: sample_tracking fixes
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1287030296 14400 # Node ID c8173a50bc9bdb0c8e07807c1b73be746557647f # Parent 4d5b00b6fe741a35320a572302d1fb8bb7eb6971 sample_tracking fixes --- a/templates/requests/common/sample_datasets.mako +++ b/templates/requests/common/sample_datasets.mako @@ -1,5 +1,5 @@ -<%def name="render_sample_datasets( cntrller, sample )"> - <a href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${sample.transferred_dataset_files} / ${len( sample.datasets )}</a> +<%def name="render_sample_datasets( sample )"> + ${sample.transferred_dataset_files} / ${len( sample.datasets )} </%def> -${render_sample_datasets( cntrller, sample )} +${render_sample_datasets( sample )} --- a/test/functional/test_forms_and_requests.py +++ b/test/functional/test_forms_and_requests.py @@ -160,8 +160,8 @@ class TestFormsAndRequests( TwillTestCas name = 'Test Requestype' self.create_request_type( name, "test sequencer configuration", - str( request_form.id ), - str( sample_form.id ), + self.security.encode_id( request_form.id ), + self.security.encode_id( sample_form.id ), sample_states, strings_displayed=[ 'Create a new sequencer configuration' ], strings_displayed_after_submit=[ "Sequencer configuration (%s) has been created" % name ] ) --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -88,7 +88,7 @@ class RequestsGrid( grids.Grid ): StateColumn( "State", key='state', filterable="advanced", - link=( lambda item: iff( item.deleted, None, dict( operation="events", id=item.id ) ) ) + link=( lambda item: iff( item.deleted, None, dict( operation="request_events", id=item.id ) ) ) ) ] columns.append( grids.MulticolFilterColumn( "Search", @@ -105,7 +105,7 @@ class RequestsGrid( grids.Grid ): class RequestsCommon( BaseController, UsesFormDefinitionWidgets ): @web.json - def sample_state_updates( self, trans, cntrller, ids=None, states=None ): + def sample_state_updates( self, trans, ids=None, states=None ): # Avoid caching trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' @@ -120,12 +120,10 @@ class RequestsCommon( BaseController, Us rval[ id ] = { "state": sample.state.name, "datasets": len( sample.datasets ), "html_state": unicode( trans.fill_template( "requests/common/sample_state.mako", - sample=sample, - cntrller=cntrller ), + sample=sample), 'utf-8' ), "html_datasets": unicode( trans.fill_template( "requests/common/sample_datasets.mako", - sample=sample, - cntrller=cntrller ), + sample=sample ), 'utf-8' ) } return rval @web.expose @@ -865,8 +863,6 @@ class RequestsCommon( BaseController, Us library_id = current_samples[ copy_sample_index][ 'library_select_field' ].get_selected( return_value=True ) folder_id = current_samples[ copy_sample_index ][ 'folder_select_field' ].get_selected( return_value=True ) name = current_samples[ copy_sample_index ][ 'name' ] + '_%i' % ( len( current_samples ) + 1 ) - library_id = 'none' - folder_id = 'none' field_values = [ val for val in current_samples[ copy_sample_index ][ 'field_values' ] ] else: # The user has not selected a sample to copy (may just be adding a sample). --- a/lib/galaxy/web/controllers/requests.py +++ b/lib/galaxy/web/controllers/requests.py @@ -52,6 +52,12 @@ class Requests( BaseController ): action='undelete_request', cntrller='requests', **kwd ) ) + if operation == "request_events": + return trans.response.send_redirect( web.url_for( controller='requests_common', + action='request_events', + cntrller='requests', + **kwd ) ) + # If there are requests that have been rejected, show a message as a reminder to the user rejected = 0 for request in trans.sa_session.query( trans.app.model.Request ) \ --- a/templates/admin/requests/view_request_type.mako +++ b/templates/admin/requests/view_request_type.mako @@ -11,7 +11,7 @@ <div class="toolForm"><div class="toolFormTitle">Sequencer configuration information</div> - <form name="view_request_type" action="${h.url_for( controller='requests_admin', action='create_request_type', rt_id=request_type.id)}" method="post" > + <form name="view_request_type" action="${h.url_for( controller='requests_admin', action='create_request_type', rt_id=trans.security.encode_id( request_type.id ))}" method="post" ><div class="form-row"><label>Name</label> ${request_type.name} --- a/templates/requests/common/manage_request.mako +++ b/templates/requests/common/manage_request.mako @@ -62,7 +62,7 @@ // Build request data var ids = [] var states = [] - $.each( sample_states, function ( id, state, cntrller ) { + $.each( sample_states, function ( id, state ) { ids.push( id ); states.push( state ); }); @@ -73,7 +73,7 @@ dataType: "json", data: { ids: ids.join( "," ), states: states.join( "," ) }, success : function ( data ) { - $.each( data, function( cntrller, id, val ) { + $.each( data, function( id, val ) { // Replace HTML var cell1 = $("#sampleState-" + id); cell1.html( val.html_state ); @@ -140,7 +140,6 @@ <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit</a> %endif <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">History</a> - <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit</a> %if is_admin: %if request.is_submitted: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> @@ -178,6 +177,13 @@ <h4><img src="/static/images/fugue/toggle-expand.png" alt="Show" onclick="showContent(this);" style="cursor:pointer;"/> Request Information</h4><div style="display:none;"> + <div class="form-row"> + <ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit request informaton</a> + </li> + </ul> + </div><table class="grid" border="0"><tbody><tr> @@ -452,7 +458,7 @@ %if sample.request.is_unsubmitted: <td>Unsubmitted</td> %else: - <td id="sampleState-${sample.id}">${render_sample_state( cntrller, sample )}</td> + <td><a id="sampleState-${sample.id}" href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${render_sample_state( sample )}</a></td> %endif %if info['library']: %if cntrller == 'requests': @@ -469,9 +475,9 @@ <td></td> %endif %if request.is_submitted or request.is_complete: - <td id="sampleDatasets-${sample.id}"> - ${render_sample_datasets( cntrller, sample )} - </td> + <td><a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}"> + ${render_sample_datasets( sample )} + </a></td> %endif %else: ${show_basic_info_form( sample_index, sample, info )} --- a/templates/requests/common/sample_state.mako +++ b/templates/requests/common/sample_state.mako @@ -1,5 +1,5 @@ -<%def name="render_sample_state( cntrller, sample )"> - <a href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${sample.state.name}</a> +<%def name="render_sample_state( sample )"> + ${sample.state.name} </%def> -${render_sample_state( cntrller, sample )} +${render_sample_state( sample )} --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -163,6 +163,11 @@ class RequestsAdmin( BaseController, Use action='manage_request', cntrller='requests_admin', **kwd ) ) + if operation == "request_events": + return trans.response.send_redirect( web.url_for( controller='requests_common', + action='request_events', + cntrller='requests_admin', + **kwd ) ) if operation == "reject": return self.reject_request( trans, **kwd ) if operation == "view_type": @@ -423,7 +428,6 @@ class RequestsAdmin( BaseController, Use request_id=request_id, folder_path=folder_path, sample_id=sample.id, - open_folder=True, message=message, status=status ) ) # Get the filenames from the remote host @@ -590,21 +594,31 @@ class RequestsAdmin( BaseController, Use FOLDER_ID=str(sample.folder.id), DATASETS=datasets ) # Send the message - conn = amqp.Connection( host=trans.app.config.amqp['host'] + ":" + trans.app.config.amqp['port'], - userid=trans.app.config.amqp['userid'], - password=trans.app.config.amqp['password'], - virtual_host=trans.app.config.amqp['virtual_host'], - insist=False ) - chan = conn.channel() - msg = amqp.Message( data.replace( '\n', '' ).replace( '\r', '' ), - content_type='text/plain', - application_headers={'msg_type': 'data_transfer'} ) - msg.properties["delivery_mode"] = 2 - chan.basic_publish( msg, - exchange=trans.app.config.amqp['exchange'], - routing_key=trans.app.config.amqp['routing_key'] ) - chan.close() - conn.close() + try: + conn = amqp.Connection( host=trans.app.config.amqp['host'] + ":" + trans.app.config.amqp['port'], + userid=trans.app.config.amqp['userid'], + password=trans.app.config.amqp['password'], + virtual_host=trans.app.config.amqp['virtual_host'], + insist=False ) + chan = conn.channel() + msg = amqp.Message( data.replace( '\n', '' ).replace( '\r', '' ), + content_type='text/plain', + application_headers={'msg_type': 'data_transfer'} ) + msg.properties["delivery_mode"] = 2 + chan.basic_publish( msg, + exchange=trans.app.config.amqp['exchange'], + routing_key=trans.app.config.amqp['routing_key'] ) + chan.close() + conn.close() + except Exception, e: + message = "Error in sending the data transfer message to the Galaxy AMQP message queue:<br/>%s" % str(e) + status = "error" + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='manage_datasets', + sample_id=trans.security.encode_id( sample.id ), + status=status, + message=message) ) + def __start_datatx( self, trans, sample, selected_sample_datasets ): datatx_user = self.__setup_datatx_user( trans, sample.library, sample.folder ) # Validate sequencer information

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galaxy-dist commit 77e13329ab8b: No longer try to display Image type (including PDF) datasets within browser. Clicking on eye icon for binary and image types will now invoke save action.
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 1286945049 14400 # Node ID 77e13329ab8b9e69089400259eb70cda9525ec80 # Parent 9f172e4713edbf4d6a22f10ad01867710cce6b00 No longer try to display Image type (including PDF) datasets within browser. Clicking on eye icon for binary and image types will now invoke save action. --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -324,56 +324,56 @@ class DatasetInterface( BaseController, if not data: raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) current_user_roles = trans.get_current_user_roles() - if trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): - if data.state == trans.model.Dataset.states.UPLOAD: - return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." ) + if not trans.app.security_agent.can_access_dataset( 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: + return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." ) + + if filename and filename != "index": + # For files in extra_files_path + file_path = os.path.join( data.extra_files_path, filename ) + if os.path.exists( file_path ): + mime, encoding = mimetypes.guess_type( file_path ) + if not mime: + try: + mime = trans.app.datatypes_registry.get_mimetype_by_extension( ".".split( file_path )[-1] ) + except: + mime = "text/plain" - if filename and filename != "index": - # For files in extra_files_path - file_path = os.path.join( data.extra_files_path, filename ) - if os.path.exists( file_path ): - mime, encoding = mimetypes.guess_type( file_path ) - if not mime: - try: - mime = trans.app.datatypes_registry.get_mimetype_by_extension( ".".split( file_path )[-1] ) - except: - mime = "text/plain" - - trans.response.set_content_type( mime ) - return open( file_path ) - else: - return "Could not find '%s' on the extra files path %s." % (filename,file_path) - - mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) - trans.response.set_content_type(mime) - trans.log_event( "Display dataset id: %s" % str( dataset_id ) ) - - if to_ext: # Saving the file - if data.ext in composite_extensions: - return self.archive_composite_dataset( trans, data, **kwd ) - else: - trans.response.headers['Content-Length'] = int( os.stat( data.file_name ).st_size ) - if to_ext[0] != ".": - to_ext = "." + to_ext - valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - fname = data.name - fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] - trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy%s-[%s]%s" % (data.hid, fname, to_ext) - return open( data.file_name ) - if os.path.exists( data.file_name ): - max_peek_size = 1000000 # 1 MB - if preview and (not isinstance(data.datatype, datatypes.binary.Binary)) and os.stat( data.file_name ).st_size > max_peek_size: - trans.response.set_content_type( "text/html" ) - return trans.stream_template_mako( "/dataset/large_file.mako", - truncated_data = open( data.file_name ).read(max_peek_size), - data = data ) - else: - return open( data.file_name ) + trans.response.set_content_type( mime ) + return open( file_path ) else: - raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % data.file_name ) + return "Could not find '%s' on the extra files path %s." % (filename,file_path) + + mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) + trans.response.set_content_type(mime) + trans.log_event( "Display dataset id: %s" % str( dataset_id ) ) + + if to_ext or isinstance(data.datatype, datatypes.binary.Binary) or isinstance(data.datatype, datatypes.images.Image): # Saving the file, or binary/image file + if data.extension in composite_extensions: + return self.archive_composite_dataset( trans, data, **kwd ) + else: + trans.response.headers['Content-Length'] = int( os.stat( data.file_name ).st_size ) + 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] + 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 ): + raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % data.file_name ) + + max_peek_size = 1000000 # 1 MB + if preview and os.stat( data.file_name ).st_size > max_peek_size: + trans.response.set_content_type( "text/html" ) + return trans.stream_template_mako( "/dataset/large_file.mako", + truncated_data = open( data.file_name ).read(max_peek_size), + data = data ) else: - return trans.show_error_message( "You are not allowed to access this dataset" ) - + return open( data.file_name ) + @web.expose @web.require_login( "see all available datasets" ) def list( self, trans, **kwargs ):

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