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galaxy-dist commit ba34d996fff5: Merge.
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 Dannon Baker <dannonbaker(a)me.com> # Date 1289568520 18000 # Node ID ba34d996fff5669eca98ff98c6035a68ac93bd34 # Parent 2389c323a1e6a50de6d48d5431d16d830ccef021 # Parent a6cd0223a53b4f9498a0dde69dcef53387188e5f Merge. --- a/templates/requests/common/events.mako +++ /dev/null @@ -1,53 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<% - is_admin = cntrller == 'requests_admin' and trans.user_is_admin() - can_edit_request = ( is_admin and not request.is_complete ) or request.is_unsubmitted - can_reject_request = is_admin and request.is_submitted - can_add_samples = request.is_unsubmitted -%> - -<br/><br/> -<ul class="manage-table-actions"> - <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request Actions</a></li> - <div popupmenu="request-${request.id}-popup"> - <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> - %if can_edit_request: - <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit this request</a> - %endif - %if can_add_samples: - <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit this request</a> - %endif - %if can_reject_request: - <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> - %endif - </div> -</ul> - -%if message: - ${render_msg( message, status )} -%endif - -<h2>History of Sequencing Request "${request.name}"</h2> - -<div class="toolForm"> - <table class="grid"> - <thead> - <tr> - <th>State</th> - <th>Last Update</th> - <th>Comments</th> - </tr> - </thead> - <tbody> - %for state, updated, comments in events_list: - <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - <td><b><a>${state}</a></b></td> - <td><a>${updated}</a></td> - <td><a>${comments}</a></td> - </tr> - %endfor - </tbody> - </table> -</div> --- a/tools/ncbi_blast_plus/blast_filter_fasta.py +++ /dev/null @@ -1,38 +0,0 @@ -#!/usr/bin/env python -"""Filter a FASTA file using tabular output, e.g. from BLAST. - -Takes five command line options, tabular BLAST filename, ID column number -(using one based counting), input FASTA filename, and two output FASTA -filenames (for records with and without any BLAST hits). - -In the default NCBI BLAST+ tabular output, the query sequence ID is in column -one, and the ID of the match from the database is in column two. -""" -import sys -from galaxy_utils.sequence.fasta import fastaReader, fastaWriter - -#Parse Command Line -blast_file, blast_col, in_file, out_positive_file, out_negative_file = sys.argv[1:] -blast_col = int(blast_col)-1 -assert blast_col >= 0 - -#Read tabular BLAST file and record all queries with hit(s) -ids = set() -blast_handle = open(blast_file, "rU") -for line in blast_handle: - ids.add(line.split("\t")[blast_col]) -blast_handle.close() - -#Write filtered FASTA file based on IDs from BLAST file -reader = fastaReader(open(in_file, "rU")) -positive_writer = fastaWriter(open(out_positive_file, "w")) -negative_writer = fastaWriter(open(out_negative_file, "w")) -for record in reader: - #The [1:] is because the fastaReader leaves the > on the identifer. - if record.identifier and record.identifier.split()[0][1:] in ids: - positive_writer.write(record) - else: - negative_writer.write(record) -positive_writer.close() -negative_writer.close() -reader.close() --- a/tools/ncbi_blast_plus/blast_filter_fasta.xml +++ /dev/null @@ -1,37 +0,0 @@ -<tool id="blast_filter_fasta" name="Filter FASTA using BLAST output" version="0.0.1"> - <description>Divide a FASTA file based on BLAST hits</description> - <command interpreter="python"> - blast_filter_fasta.py $blast_file $blast_col $in_file $out_positive_file $out_negative_file - </command> - <inputs> - <param name="in_file" type="data" format="fasta" label="FASTA file to filter"/> - <param name="blast_file" type="data" format="tabular" label="Tabular BLAST output"/> - <param name="blast_col" type="select" label="Column containing FASTA identifiers"> - <option value="1">Column 1 - BLAST query ID</option> - <option value="2">Column 2 - BLAST match ID</option> - </param> - </inputs> - <outputs> - <data name="out_positive_file" format="fasta" label="Sequences with BLAST hits" /> - <data name="out_negative_file" format="fasta" label="Sequences without BLAST hits" /> - </outputs> - <requirements> - </requirements> - <tests> - </tests> - <help> - -**What it does** - -Typical use would be to take a multi-sequence FASTA and the tabular output of -running BLAST on it, and divide the FASTA file in two: those sequence with a -BLAST hit, and those without. - -In the default NCBI BLAST+ tabular output, the query sequence ID is in column -one, and the ID of the match from the database is in column two. - -This allows you to filter the FASTA file for the subjects in the BLAST search, -rather than filtering the FASTA file for the queries in the BLAST search. - - </help> -</tool>

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galaxy-dist commit dbe6ab1eaa7c: merge
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1289568820 18000 # Node ID dbe6ab1eaa7ca7f9754c22bb2f6edd3fc26e3432 # Parent b5b6b92a71e960691bb514af32ba2e21a731bd4e # Parent ba34d996fff5669eca98ff98c6035a68ac93bd34 merge

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galaxy-dist commit b124f54952de: Small fixes and refactor to workflows: remove unused ensure_popup_helper(), and fix extra comma that was returning error in IE.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

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

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galaxy-dist commit b7f712cecaa9: Prevent Rename Dataset Action from allowing a blank input.
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 Dannon Baker <dannonbaker(a)me.com> # Date 1289590343 18000 # Node ID b7f712cecaa9f527f1161f923ebe798eba526cb6 # Parent fc1f67023d86a69ea7229501b093d61748630f4c Prevent Rename Dataset Action from allowing a blank input. --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -60,14 +60,12 @@ class DefaultJobAction(object): class EmailAction(DefaultJobAction): name = "EmailAction" verbose_name = "Email Notification" - @classmethod def execute(cls, app, sa_session, action, job): smtp_server = app.config.smtp_server - if action.action_arguments: - if action.action_arguments.has_key('host'): - host = action.action_arguments['host'] + if action.action_arguments and action.action_arguments.has_key('host'): + host = action.action_arguments['host'] else: host = 'usegalaxy.org' if smtp_server is None: @@ -107,9 +105,8 @@ class EmailAction(DefaultJobAction): @classmethod def get_short_str(cls, pja): - if pja.action_arguments: - if pja.action_arguments.has_key('host'): - return "Email the current user from server %s when this job is complete." % pja.action_arguments['host'] + if pja.action_arguments and pja.action_arguments.has_key('host'): + return "Email the current user from server %s when this job is complete." % pja.action_arguments['host'] else: return "Email the current user when this job is complete." @@ -153,9 +150,11 @@ class RenameDatasetAction(DefaultJobActi @classmethod def execute(cls, app, sa_session, action, job): - for dataset_assoc in job.output_datasets: - if action.output_name == '' or dataset_assoc.name == action.output_name: - dataset_assoc.dataset.name = action.action_arguments['newname'] + # Prevent renaming a dataset to the empty string. + if action.action_arguments and action.action_arguments.has_key('newname') and action.action_arguments['newname'] != '': + for dataset_assoc in job.output_datasets: + if action.output_name == '' or dataset_assoc.name == action.output_name: + dataset_assoc.dataset.name = action.action_arguments['newname'] @classmethod def get_config_form(cls, trans): @@ -173,7 +172,11 @@ class RenameDatasetAction(DefaultJobActi @classmethod def get_short_str(cls, pja): - return "Rename output '%s' to '%s'." % (pja.output_name, pja.action_arguments['newname']) + # Prevent renaming a dataset to the empty string. + if pja.action_arguments and pja.action_arguments.has_key('newname') and pja.action_arguments['newname'] != '': + return "Rename output '%s' to '%s'." % (pja.output_name, pja.action_arguments['newname']) + else: + return "Rename action used without a new name specified. Output name will be unchanged." class HideDatasetAction(DefaultJobAction):

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galaxy-dist commit 2389c323a1e6: Fix for compatibility with the refactored base job runner build_command_line.
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 Dannon Baker <dannonbaker(a)me.com> # Date 1289568484 18000 # Node ID 2389c323a1e6a50de6d48d5431d16d830ccef021 # Parent ca23ea683d26df004e666ede82950c712e3ac637 Fix for compatibility with the refactored base job runner build_command_line. DRMAA runner now uses get_id_tag() in *Wrapper instead of job_id directly for creation of .sh .o and .e files, as well as some debugging. This fixes the issue where many tasks for the same job get submitted at the same time and these files overwrite one another or collide in the submission process. --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -295,6 +295,10 @@ class JobWrapper( object ): def get_job( self ): return self.sa_session.query( model.Job ).get( self.job_id ) + def get_id_tag(self): + # For compatability with drmaa, which uses job_id right now, and TaskWrapper + return str(self.job_id) + def get_param_dict( self ): """ Restore the dictionary of parameters from the database. @@ -788,6 +792,10 @@ class TaskWrapper(JobWrapper): def get_task( self ): return self.sa_session.query(model.Task).get(self.task_id) + def get_id_tag(self): + # For compatibility with drmaa job runner and TaskWrapper, instead of using job_id directly + return "%s_%s" % (self.job_id, self.task_id) + def get_param_dict( self ): """ Restore the dictionary of parameters from the database. @@ -964,7 +972,7 @@ class TaskWrapper(JobWrapper): def setup_external_metadata( self, exec_dir = None, tmp_dir = None, dataset_files_path = None, config_root = None, datatypes_config = None, set_extension = True, **kwds ): # There is no metadata setting for tasks. This is handled after the merge, at the job level. - pass + return "" @property def user( self ): --- a/lib/galaxy/jobs/runners/tasks.py +++ b/lib/galaxy/jobs/runners/tasks.py @@ -117,8 +117,12 @@ class TaskedJobRunner( object ): basic.merge(working_directory, output_filename) log.debug('execution finished: %s' % command_line) for tw in task_wrappers: - stdout += tw.get_task().stdout - stderr += tw.get_task().stderr + # Prevent repetitive output, e.g. "Sequence File Aligned"x20 + # Eventually do a reduce for jobs that output "N reads mapped", combining all N for tasks. + if stdout.strip() != tw.get_task().stdout.strip(): + stdout += tw.get_task().stdout + if stderr.strip() != tw.get_task().stderr.strip(): + stderr += tw.get_task().stderr except Exception: job_wrapper.fail( "failure running job", exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -125,7 +125,7 @@ class DRMAAJobRunner( BaseJobRunner ): command_line = self.build_command_line( job_wrapper, include_metadata=True ) except: job_wrapper.fail( "failure preparing job", exception=True ) - log.exception("failure running job %d" % job_wrapper.job_id) + log.exception("failure running job %d" % job_wrapper.get_id_tag()) return runner_url = job_wrapper.tool.job_runner @@ -137,7 +137,7 @@ class DRMAAJobRunner( BaseJobRunner ): # Check for deletion before we change state if job_wrapper.get_state() == model.Job.states.DELETED: - log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.job_id ) + log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.get_id_tag() ) job_wrapper.cleanup() return @@ -145,10 +145,10 @@ class DRMAAJobRunner( BaseJobRunner ): job_wrapper.change_state( model.Job.states.QUEUED ) # define job attributes - ofile = "%s/database/pbs/%s.o" % (os.getcwd(), job_wrapper.job_id) - efile = "%s/database/pbs/%s.e" % (os.getcwd(), job_wrapper.job_id) + ofile = "%s/database/pbs/%s.o" % (os.getcwd(), job_wrapper.get_id_tag()) + efile = "%s/database/pbs/%s.e" % (os.getcwd(), job_wrapper.get_id_tag()) jt = self.ds.createJobTemplate() - jt.remoteCommand = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job_wrapper.job_id) + jt.remoteCommand = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job_wrapper.get_id_tag()) jt.outputPath = ":%s" % ofile jt.errorPath = ":%s" % efile native_spec = self.get_native_spec( runner_url ) @@ -163,14 +163,16 @@ class DRMAAJobRunner( BaseJobRunner ): # job was deleted while we were preparing it if job_wrapper.get_state() == model.Job.states.DELETED: - log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.job_id ) + log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.get_id_tag() ) self.cleanup( ( ofile, efile, jt.remoteCommand ) ) job_wrapper.cleanup() return - galaxy_job_id = job_wrapper.job_id - log.debug("(%s) submitting file %s" % ( galaxy_job_id, jt.remoteCommand ) ) - log.debug("(%s) command is: %s" % ( galaxy_job_id, command_line ) ) + # wrapper.get_id_tag() instead of job_id for compatibility with TaskWrappers. + galaxy_id_tag = job_wrapper.get_id_tag() + + log.debug("(%s) submitting file %s" % ( galaxy_id_tag, jt.remoteCommand ) ) + log.debug("(%s) command is: %s" % ( galaxy_id_tag, command_line ) ) # runJob will raise if there's a submit problem job_id = self.ds.runJob(jt) log.info("(%s) queued as %s" % ( galaxy_job_id, job_id ) )

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galaxy-dist commit a6cd0223a53b: Add -parse_deflines switch to BLAST+ wrappers
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 1287758911 -3600 # Node ID a6cd0223a53b4f9498a0dde69dcef53387188e5f # Parent 082399b4681b878d20a727150832ef30679b7e1c Add -parse_deflines switch to BLAST+ wrappers --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -27,6 +27,7 @@ blastn -word_size $adv_opts.word_size #end if $adv_opts.ungapped +$adv_opts.parse_deflines ## End of advanced options: #end if </command> @@ -99,6 +100,7 @@ blastn <validator type="in_range" min="0" /></param><param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -28,6 +28,7 @@ blastp #end if ##Ungapped disabled for now - see comments below ##$adv_opts.ungapped +$adv_opts.parse_deflines ## End of advanced options: #end if </command> @@ -104,6 +105,7 @@ blastp Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.' <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> --> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -26,6 +26,7 @@ tblastx #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): -word_size $adv_opts.word_size #end if +$adv_opts.parse_deflines ## End of advanced options: #end if </command> @@ -97,6 +98,7 @@ tblastx <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="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -27,6 +27,7 @@ blastx -word_size $adv_opts.word_size #end if $adv_opts.ungapped +$adv_opts.parse_deflines ## End of advanced options: #end if </command> @@ -99,6 +100,7 @@ blastx <validator type="in_range" min="0" /></param><param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -27,6 +27,7 @@ tblastn #end if ##Ungapped disabled for now - see comments below ##$adv_opts.ungapped +$adv_opts.parse_deflines ## End of advanced options: #end if </command> @@ -99,6 +100,7 @@ tblastn Tried using '-ungapped -comp_based_stats F' and tblastn crashed with 'Attempt to access NULL pointer.' <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> --> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/></when></conditional></inputs>

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galaxy-dist commit b5b6b92a71e9: Refactored tracks/data function into multiple helper functions that can be reused as needed.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1289568743 18000 # Node ID b5b6b92a71e960691bb514af32ba2e21a731bd4e # Parent a6cd0223a53b4f9498a0dde69dcef53387188e5f Refactored tracks/data function into multiple helper functions that can be reused as needed. --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -7,7 +7,7 @@ pkg_resources.require( "bx-python" ) from bx.seq.twobit import TwoBitFile from galaxy import model -from galaxy.util.json import to_json_string, from_json_string +from galaxy.util.json import from_json_string from galaxy.web.base.controller import * from galaxy.web.framework import simplejson from galaxy.web.framework.helpers import grids @@ -249,29 +249,21 @@ class TracksController( BaseController, """ Called by the browser to request a block of data """ + + # Parameter check. + if not chrom: + return messages.NO_DATA + + # Dataset check. dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id ) - if not dataset or not chrom: - return messages.NO_DATA - if dataset.state == trans.app.model.Job.states.ERROR: - return messages.ERROR - if dataset.state != trans.app.model.Job.states.OK: - return messages.PENDING - - track_type, data_sources = dataset.datatype.get_track_type() - for source_type, data_source in data_sources.iteritems(): - try: - converted_dataset = dataset.get_converted_dataset(trans, data_source) - except ValueError: - return messages.NO_CONVERTER - - # Need to check states again for the converted version - if converted_dataset and converted_dataset.state == model.Dataset.states.ERROR: - job_id = trans.sa_session.query( trans.app.model.JobToOutputDatasetAssociation ).filter_by( dataset_id=converted_dataset.id ).first().job_id - job = trans.sa_session.query( trans.app.model.Job ).get( job_id ) - return { 'kind': messages.ERROR, 'message': job.stderr } - - if not converted_dataset or converted_dataset.state != model.Dataset.states.OK: - return messages.PENDING + msg = self._check_dataset_state( trans, dataset ) + if msg: + return msg + + # Get converted datasets. + data_sources, message = self._get_converted_datasets( trans, dataset ) + if not data_sources: + return message extra_info = None if 'index' in data_sources: @@ -365,4 +357,43 @@ class TracksController( BaseController, @web.expose def list_tracks( self, trans, **kwargs ): return self.tracks_grid( trans, **kwargs ) - + + + # + # Helper methods. + # + + def _check_dataset_state( self, trans, dataset ): + """ + Returns a message if dataset is not ready to be used in visualization. + """ + if not dataset: + return messages.NO_DATA + if dataset.state == trans.app.model.Job.states.ERROR: + return messages.ERROR + if dataset.state != trans.app.model.Job.states.OK: + return messages.PENDING + return None + + def _get_converted_datasets( self, trans, dataset ): + """ + Returns (a) converted datasets for a dataset and (b) dictionary of + any messages based on or derived from the conversion. + """ + track_type, data_sources = dataset.datatype.get_track_type() + for source_type, data_source in data_sources.iteritems(): + try: + converted_dataset = dataset.get_converted_dataset(trans, data_source) + except ValueError: + return None, messages.NO_CONVERTER + + # Need to check states again for the converted version + if converted_dataset and converted_dataset.state == model.Dataset.states.ERROR: + job_id = trans.sa_session.query( trans.app.model.JobToOutputDatasetAssociation ).filter_by( dataset_id=converted_dataset.id ).first().job_id + job = trans.sa_session.query( trans.app.model.Job ).get( job_id ) + return None, { 'kind': messages.ERROR, 'message': job.stderr } + + if not converted_dataset or converted_dataset.state != model.Dataset.states.OK: + return None, messages.PENDING + + return data_sources, None

1 0

galaxy-dist commit f2383b761f4e: Make sure samples have associated target libraries befoe enabling ability to transfer datasets, use better naming convention for request history code and templates, eliminate the ability to submit a request unless it has samples.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

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

1 0

galaxy-dist commit ff7327f2946e: When generating the list of target libraries for transferring sample datasets, use all libraries accessible to the request's user rather than all libraries for which that user has LIBRARY_ADD permission.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

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

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galaxy-dist commit 0f6ace5c397b: Ignore backup files from some editors
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1286965717 -3600 # Node ID 0f6ace5c397b000993db8e491a33e42423cdc807 # Parent d8184d91928c83f0269bd0267be949bc5d676e8b Ignore backup files from some editors --- a/.hgignore +++ b/.hgignore @@ -43,4 +43,4 @@ run_functional_tests.html *.orig .DS_Store *.rej - +*~

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galaxy-dist commit d8184d91928c: Remove FASTA filter script from BLAST+ tools (I want to generalise it)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

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

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galaxy-dist commit 082399b4681b: Remove broken blastn test
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 1288001263 -3600 # Node ID 082399b4681b878d20a727150832ef30679b7e1c # Parent 0f6ace5c397b000993db8e491a33e42423cdc807 Remove broken blastn test --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -119,20 +119,6 @@ blastn <requirement type="binary">blastn</requirement></requirements><tests> - <test> - <param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/> -  - <param name="database" value="phiX" /> - <param name="blast_type" value="megablast" /> -  - <param name="evalue_cutoff" value="10.0" /> - <param name="filter_query" value="yes" /> - <param name="out_format" value="6" /> - <output name="output1" file="megablast_wrapper_test1.out"/> - </test></tests><help>

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galaxy-dist commit 5c212dfc6189: Fix a caption capitalisation
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

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

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galaxy-dist commit dfc848840870: Various sample tracking bug fixes: samples no longer require bar codes, change all references to 'barcode' to be 'bar_code' since that is what the model uses, and mixing the 2 is not maintainable, enhance sample popup menu options, fix broken logic that handles bulk sample library and folderr changes.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

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

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galaxy-dist commit 122aaabe2c7e: Workaround Issue 397 using 'if' in Cheetah template to avoid hidden parameters
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

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

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galaxy-dist commit caed55b53f5a: Allows the downloading of metadata files associated with datasets (such as bai indices for bam files). This is done by adding a dropdown menu to the Save icon of appropriate datasets. Could potentially be modified to access implicitly converted datatypes as well in the future. Closes #410
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

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

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galaxy-dist commit 10d0ffe5b7e2: Include BLAST-XML to tabular in tool_conf.xml.sample
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

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

1 0

galaxy-dist commit 0e5144e49c14: Trackster: packed scripts, support LEN files that are space separated
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 James Taylor <james(a)jamestaylor.org> # Date 1289414596 18000 # Node ID 0e5144e49c14eb2a77e1d3182a33b4f9c8de98fc # Parent d56f296aaa610a537d35cb7d235eac9d8f596464 Trackster: packed scripts, support LEN files that are space separated --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -220,9 +220,10 @@ class TracksController( BaseController, if not os.path.exists( len_file ): return None for line in open( len_file ): - if line.startswith("#"): continue - line = line.rstrip("\r\n") - fields = line.split("\t") + if line.startswith("#"): + continue + # LEN files are just whitespace separated + fields = line.split() manifest[fields[0]] = int(fields[1]) return manifest --- 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=50,CONNECTOR_COLOR="#ccc",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...",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;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.createPa ttern(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()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,d,c,b){this.container=a;this.vis_id=c;this.dbkey=b;this.ti tle=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init();this.reset()};$.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=$("<div/>").addClas s("overview-viewport").appendTo(this.overview);this.overview_close=$("<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=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<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.wh ich)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<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(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}a.chrom_select.html(h);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 e=0,d=a.tracks.length;e<d;e++){a.tracks[e].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.original_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=$(this);var i=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(i/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<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($(this))}).bind("drag ",function(i){var f=Math.min(i.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(i.clientX,this.drag_origin_x)-a.container.offset().left,h=(a.high-a.low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(j){var f=Math.min(j.clientX,this.drag_origin_x),d=Math.max(j.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),i=a.low;a.low=Math.round(f/g*h)+i;a.high=Math.round(d/g*h)+i;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+c ommatize(b))},change_chrom:function(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counte r;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(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())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;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_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(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);th is.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.nav_container.height()-45);this.nav_container.width(this.container.width());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 Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b ){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,d,c){this.name=b;this.view=a;this.parent_element=d;this.filters=(c!==undefined?get_filters(c):[]);this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<div />").addClass("track").css("position","relative");i f(!this.hidden){this.header_div=$("<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.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.filtering_div=$("<div class='track-filters'>").appendTo(this.container_div);this.filtering_div.hide();this.filtering_div.bind("drag",function(i){i.stopPropagation()});var b=$("<table class='filters'>").appendTo(this.filtering_div);var c=this;for(var e=0;e<this.filters.length;e++){var a=this.filters[e];var f=$("<tr>").appendTo(b);var g=$("<th class='filter-info'>").appendTo(f);var j=$("<span class='name'>").appendTo(g);j.text(a.name+" ");var d=$("<span class='values'>").appendTo(g);var h=$("<td>").appendTo(f);a.control_element=$("<div id='"+a.name+"-filter-control' style='width: 200 px; position: relative'>").appendTo(h);a.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(k,l){var i=l.values;d.text("["+i[0]+"-"+i[1]+"]");a.low=i[0];a.high=i[1];c.draw(true)},change:function(i,k){a.control_element.slider("option","slide").call(a.control_element,i,k)}});a.slider=a.control_element;a.slider_label=d}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 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 b=this,j=b.view;if(b.hidden){return}if(b.display_modes!==undefined){if(b.mode_div===undefined){b.mode_div=$("<div class='right-float menubutton popup' />").appendTo(b.header_div);var e= b.display_modes[0];b.mode=e;b.mode_div.text(e);var c=function(i){b.mode_div.text(i);b.mode=i;b.tile_cache.clear();b.draw()};var a={};for(var f=0,h=b.display_modes.length;f<h;f++){var g=b.display_modes[f];a[g]=function(i){return function(){c(i)}}(g)}make_popupmenu(b.mode_div,a)}else{b.mode_div.hide()}}var d={};d["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();b.is_overview=true;b.set_overview();for(var i in j.tracks){if(j.tracks[i]!==b){j.tracks[i].is_overview=false}}};d["Edit configuration"]=function(){var l=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){b.update_options(b.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},k=function(m){if((m.keyCode||m.which)===27){l()}else{if((m.keyCode||m.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",k);show_modal("Configure Track",b.gen_options(b.track_id),{Cancel:l,OK:i})};if(b.filters.length>0){d["Show filters"]=function(){var i;if(!b.filter ing_div.is(":visible")){i="Hide filters";b.filters_visible=true}else{i="Show filters";b.filters_visible=false}$("#"+b.name_div.attr("id")+"-menu").find("li").eq(2).text(i);b.filtering_div.toggle()}}d.Remove=function(){j.remove_track(b);if(j.num_tracks===0){$("#no-tracks").show()}};b.popup_menu=make_popupmenu(b.name_div,d);show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var k=this.view.low,g=this.view.high,h=g-k,f=this.view.resolution;var n=$("<div style='position: relative;'></div>"),o=this.content_div.width()/h;this.content_div.append(n);this.max_height=0;var b=Math.floor(k/f/DENSITY);var j={};while((b*DENSITY*f)<g){var l=this.content_div.width()+"_"+o+"_"+b;var e=this.tile_cache.get(l);if(!a&&e){var i=b*DENSITY*f;var d=(i-k)*o;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,n)}else{this.delayed_draw(this,l,k,g,b,f,n,o,j)}b+=1}var c=this;var m=setInterval(functio n(){if(obj_length(j)===0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var p=0;p<c.filters.length;p++){c.filters[p].update_ui_elt()}clearInterval(m)}},50)},delayed_draw:function(c,h,g,e,b,d,i,j,f){var a=setTimeout(function(){if(g<=c.view.high&&e>=c.view.low){var k=c.draw_tile(d,b,i,j);if(k){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(k).clone();var n=k.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,k);c.show_tile(k,i)}}delete f[a]},50);f[a]=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show |Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(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($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_di v.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.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;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.dat a_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),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,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=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";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={color:"black",min_value:undefined,max_value:undefined,mode:this.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.ver tical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f= (b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.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){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,w=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(w)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(w);if(!v){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;n.beginPath();n.fillStyle=this.prefs.co lor;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(d-(h-k)/m*d);n.fillRect(u,h,f,d-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,d)}n.fill()}else{n.stroke()}c.append(b);return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></i nput>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,e,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container,e);TiledTrack.call(this);this.height_p x=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true}};$.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.vie w.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,b,q){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=q;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,y=[],h=0,n=this.view.max_low;var A=[];if(this.inc_slots[a].mode!==q){delete this.inc_slots[a];this.inc_slots[a]={mode:q,w_scale:m};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var v=0,w=g.length;v<w;v++){var f=g[v],l=f[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);A.push(this.inc_slots[a][l])}else{y.push(v)}}for(var v=0,w=y.length;v<w;v++){var f=g[y[v]],l=f[0],r=f[1],c=f[2],p=f[3],d=Math.floor((r-n)*m),e=Math.ceil((c-n)*m);if(p!==undefined&&!b){var s=CONTEXT.measureText(p).width;if(d-s<0){e+=s}else{d-=s}}var u=0;while(u<=MAX_FEATURE_DEPTH){var o=true;if(this.s_e_by_tile[a][u]!==undefined){for(var t=0,z=this.s_e_by_tile[a][u].length;t<z;t++){var x=this.s_e_ by_tile[a][u][t];if(e>x[0]&&d<x[1]){o=false;break}}}if(o){if(this.s_e_by_tile[a][u]===undefined){this.s_e_by_tile[a][u]=[]}this.s_e_by_tile[a][u].push([d,e]);this.inc_slots[a][l]=u;h=Math.max(h,u);break}u++}}return h},rect_or_text:function(r,l,t,b,q,f,i,e){r.textAlign="center";var k=0,p=Math.round(l/2);for(var m=0,s=i.length;m<s;m++){var j=i[m],d="MIDNSHP"[j[0]],n=j[1];if(d==="H"||d==="S"){k-=n}var g=q+k,w=Math.floor(Math.max(0,(g-t)*l)),h=Math.floor(Math.max(0,(g+n-t)*l));switch(d){case"S":case"H":case"M":var o=f.slice(k,n);if((this.mode==="Pack"||this.mode==="Auto")&&f!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(w+this.left_offset,e+1,h-w,9);r.fillStyle=CONNECTOR_COLOR;for(var u=0,a=o.length;u<a;u++){if(g+u>=t&&g+u<=b){var v=Math.floor(Math.max(0,(g+u-t)*l));r.fillText(o[u],v+this.left_offset+p,e+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(w+this.left_offset,e+4,h-w,3)}break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(w+this.lef t_offset,e+5,h-w,1);break;case"D":r.fillStyle="red";r.fillRect(w+this.left_offset,e+4,h-w,3);break;case"P":case"I":break}k+=n}},draw_tile:function(ag,o,s,av){var N=o*DENSITY*ag,al=(o+1)*DENSITY*ag,M=al-N;var an=(!this.initial_canvas?"initial":N+"_"+al);var I=this.data_cache.get(an);var e;if(I===undefined||(this.mode!=="Auto"&&I.dataset_type==="summary_tree")){this.data_queue[[N,al]]=true;this.get_data(N,al);return}var a=Math.ceil(M*av),ai=this.prefs.label_color,l=this.prefs.block_color,r=this.mode,z=25,ae=(r==="Squish")||(r==="Dense")&&(r!=="Pack")||(r==="Auto"&&(I.extra_info==="no_detail")),W=this.left_offset,au,D,aw;var q=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(q)}q=$(q);if(I.dataset_type==="summary_tree"){D=this.summary_draw_height}else{if(r==="Dense"){D=z;aw=10}else{aw=(ae?this.vertical_nodetail_px:this.vertical_detail_px);var A=(av<0.0001?1/this.view.zoom_res:av);D=this.incremental_slots(A,I.data,ae,r)*aw+z;au=this.i nc_slots[A]}}q.css({position:"absolute",top:0,left:(N-this.view.low)*av-W});q.get(0).width=a+W;q.get(0).height=D;s.parent().css("height",Math.max(this.height_px,D)+"px");var J=q.get(0).getContext("2d");J.fillStyle=l;J.font=this.default_font;J.textAlign="right";this.container_div.find(".yaxislabel").remove();if(I.dataset_type=="summary_tree"){var Y=I.data,L=I.max,b=Math.ceil(I.delta*av);var p=$("<div />").addClass("yaxislabel").text(L);p.css({position:"absolute",top:"22px",left:"10px"});p.prependTo(this.container_div);for(var ap=0,H=Y.length;ap<H;ap++){var aa=Math.floor((Y[ap][0]-N)*av);var Z=Y[ap][1];if(!Z){continue}var am=Z/L*this.summary_draw_height;J.fillStyle="black";J.fillRect(aa+W,this.summary_draw_height-am,b,am);if(this.prefs.show_counts&&J.measureText(Z).width<b){J.fillStyle="#bbb";J.textAlign="center";J.fillText(Z,aa+W+(b/2),this.summary_draw_height-5)}}e="Summary";s.append(q);return q}if(I.message){q.css({border:"solid red","border-width":"2px 2px 2px 0px"});J.fil lStyle="red";J.textAlign="left";J.fillText(I.message,100+W,aw)}var ad=false;if(I.data){ad=true;for(var ar=0;ar<this.filters.length;ar++){if(!this.filters[ar].applies_to(I.data[0])){ad=false}}}if(ad){q.addClass(FILTERABLE_CLASS)}var at=I.data;var ao=0;for(var ap=0,H=at.length;ap<H;ap++){var S=at[ap],R=S[0],aq=S[1],ac=S[2],O=S[3];if(au[R]===undefined){continue}var ab=false;var U;for(var ar=0;ar<this.filters.length;ar++){U=this.filters[ar];U.update_attrs(S);if(!U.keep(S)){ab=true;break}}if(ab){continue}if(aq<=al&&ac>=N){var af=Math.floor(Math.max(0,(aq-N)*av)),K=Math.ceil(Math.min(a,Math.max(0,(ac-N)*av))),X=(r==="Dense"?1:(1+au[R]))*aw;var G,aj,P=null,ax=null;if(I.dataset_type==="bai"){var v=S[4];J.fillStyle=l;if(S[5] instanceof Array){var E=Math.floor(Math.max(0,(S[5][0]-N)*av)),Q=Math.ceil(Math.min(a,Math.max(0,(S[5][1]-N)*av))),C=Math.floor(Math.max(0,(S[6][0]-N)*av)),w=Math.ceil(Math.min(a,Math.max(0,(S[6][1]-N)*av)));if(S[5][1]>=N&&S[5][0]<=al){this.rect_or_text(J,av,N,al ,S[5][0],S[5][2],v,X)}if(S[6][1]>=N&&S[6][0]<=al){this.rect_or_text(J,av,N,al,S[6][0],S[6][2],v,X)}if(C>Q){J.fillStyle=CONNECTOR_COLOR;J.fillRect(Q+W,X+5,C-Q,1)}}else{J.fillStyle=l;this.rect_or_text(J,av,N,al,aq,O,v,X)}if(r!=="Dense"&&!ae&&aq>N){J.fillStyle=this.prefs.label_color;if(o===0&&af-J.measureText(O).width<0){J.textAlign="left";J.fillText(R,K+2+W,X+8)}else{J.textAlign="right";J.fillText(R,af-2+W,X+8)}J.fillStyle=l}}else{if(I.dataset_type==="interval_index"){if(ae){J.fillStyle=l;J.fillRect(af+W,X+5,K-af,1)}else{var F=S[4],V=S[5],ah=S[6],h=S[7];if(V&&ah){P=Math.floor(Math.max(0,(V-N)*av));ax=Math.ceil(Math.min(a,Math.max(0,(ah-N)*av)))}if(r!=="Dense"&&O!==undefined&&aq>N){J.fillStyle=ai;if(o===0&&af-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+W,X+8)}else{J.textAlign="right";J.fillText(O,af-2+W,X+8)}J.fillStyle=l}if(h){if(F){if(F=="+"){J.fillStyle=RIGHT_STRAND}else{if(F=="-"){J.fillStyle=LEFT_STRAND}}J.fillRect(af+W,X,K-af,10);J.fillStyle=l}for(var an =0,g=h.length;an<g;an++){var u=h[an],d=Math.floor(Math.max(0,(u[0]-N)*av)),T=Math.ceil(Math.min(a,Math.max((u[1]-N)*av)));if(d>T){continue}G=5;aj=3;J.fillRect(d+W,X+aj,T-d,G);if(P!==undefined&&!(d>ax||T<P)){G=9;aj=1;var ak=Math.max(d,P),B=Math.min(T,ax);J.fillRect(ak+W,X+aj,B-ak,G)}}}else{G=9;aj=1;J.fillRect(af+W,X+aj,K-af,G);if(S.strand){if(S.strand=="+"){J.fillStyle=RIGHT_STRAND_INV}else{if(S.strand=="-"){J.fillStyle=LEFT_STRAND_INV}}J.fillRect(af+W,X,K-af,10);J.fillStyle=l}}}}else{if(I.dataset_type==="vcf"){if(ae){J.fillStyle=l;J.fillRect(af+W,X+5,K-af,1)}else{var t=S[4],n=S[5],c=S[6];G=9;aj=1;J.fillRect(af+W,X,K-af,G);if(r!=="Dense"&&O!==undefined&&aq>N){J.fillStyle=ai;if(o===0&&af-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+W,X+8)}else{J.textAlign="right";J.fillText(O,af-2+W,X+8)}J.fillStyle=l}var m=t+" / "+n;if(aq>N&&J.measureText(m).width<(K-af)){J.fillStyle="white";J.textAlign="center";J.fillText(m,W+af+(K-af)/2,X+8);J.fillStyle=l}}}}}ao++}}return q },gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_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=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_ counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,e,c){FeatureTrack.call(this,d,b,a,e,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); +var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=50,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset.",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPa ttern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.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,d,c,b,e){this.container=a;this.vis_id=c;this.dbkey=b;this. title=d;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(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top _container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<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(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-a utocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").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(funct ion(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(f){if(f.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=f.chrom_info;var j='<option value="">Select Chrom/Contig</option>';for(var h=0,e=a.chrom_data.length;h<e;h++){var g=a.chrom_data[h].chrom;j+='<option value="'+g+'">'+g+"</option>"}a.chrom_select.html(j);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});if(d){d()}},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f){this.current_x=f.offsetX}).bind("drag",function(f){var h=f.offsetX-this.current_x;this.current_x=f.offsetX;var g=Math.round(h/a.viewport_container .width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(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(f){this.original_low=a.low;this.current_height=f.clientY;this.current_x=f.offsetX;this.enable_pan=(f.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(h){if(!this.enable_pan||this.in_reordering){return}var f=$(this);var j=h.offsetX-this.current_x;var g=f.scrollTop()-(h.clientY-this.current_height);f.scrollTop(g);this.current_height=h.clientY;this.current_x=h.offsetX;var i=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)});this.top_labeltrack.bind("dragstart",function(f){this.drag_origin_x=f.clientX;this.drag_origin_pos=f.clientX/a.viewport_container.width()*(a.high-a.low)+ a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var g=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,f=Math.max(j.clientX,this.drag_origin_x)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low);this.drag_div.css({left:g+"px",width:(f-g)+"px"})}).bind("dragend",function(k){var g=Math.min(k.clientX,this.drag_origin_x),f=Math.max(k.clientX,this.drag_origin_x),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window( )});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},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(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b= a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(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())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;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_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(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()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());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 Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.sli der_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="f loat"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,d,c){this.name=b;this.view=a;this.parent_element=d;this.filters=(c!==undefined?get_filters(c):[]);this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<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.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.filtering_div=$("<div class='track-filters'>").appendTo(this.container_div);this.filtering_div.hide();this.filtering_div.bind("drag",function(i){i.stopPropagation()});var b=$("<table class='filters'>").appendTo(this.filtering_div);var c=this;for(va r e=0;e<this.filters.length;e++){var a=this.filters[e];var f=$("<tr>").appendTo(b);var g=$("<th class='filter-info'>").appendTo(f);var j=$("<span class='name'>").appendTo(g);j.text(a.name+" ");var d=$("<span class='values'>").appendTo(g);var h=$("<td>").appendTo(f);a.control_element=$("<div id='"+a.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(h);a.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(k,l){var i=l.values;d.text("["+i[0]+"-"+i[1]+"]");a.low=i[0];a.high=i[1];c.draw(true)},change:function(i,k){a.control_element.slider("option","slide").call(a.control_element,i,k)}});a.slider=a.control_element;a.slider_label=d}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_di v.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.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 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 b=this,j=b.view;if(b.hidden){return}if(b.display_modes!==undefined){if(b.mode_div===undefined){b.mode_div=$("<div class='right-float menubutton popup' />").appendTo(b.header_div);var e=b.display_modes[0];b.mode=e;b.mode_div.text(e);var c=function(i){b.mode_div.text(i);b.mode=i;b.tile_cache.clear();b.draw()};var a={};for(var f=0,h=b.display_modes.length;f<h;f++){var g=b.display_modes[f];a[g]=function(i){return function(){c(i)}}(g)}make_popupmenu(b.mode_div,a)}else{b.mode_div.hide()}}var d={};d["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();b.is_overview=true;b.set_overview();for(var i in j.tracks){if(j.tracks[i]!==b){j.tracks[i].is_overview=false}}};d["Edit configuration"]=function(){var l=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){b.update_options(b.track_ id);hide_modal();$(window).unbind("keypress.check_enter_esc")},k=function(m){if((m.keyCode||m.which)===27){l()}else{if((m.keyCode||m.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",k);show_modal("Configure Track",b.gen_options(b.track_id),{Cancel:l,OK:i})};if(b.filters.length>0){d["Show filters"]=function(){var i;if(!b.filtering_div.is(":visible")){i="Hide filters";b.filters_visible=true}else{i="Show filters";b.filters_visible=false}$("#"+b.name_div.attr("id")+"-menu").find("li").eq(2).text(i);b.filtering_div.toggle()}}d.Remove=function(){j.remove_track(b);if(j.num_tracks===0){$("#no-tracks").show()}};b.popup_menu=make_popupmenu(b.name_div,d);show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var k=this.view.low,g=this.view.high,h=g-k,f=this.view.resolution;var n=$("<div style='position: relative;'></div>"),o=this.content_div.width()/h;this.content_div.append(n);this.max_height= 0;var b=Math.floor(k/f/DENSITY);var j={};while((b*DENSITY*f)<g){var l=this.content_div.width()+"_"+o+"_"+b;var e=this.tile_cache.get(l);if(!a&&e){var i=b*DENSITY*f;var d=(i-k)*o;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,n)}else{this.delayed_draw(this,l,k,g,b,f,n,o,j)}b+=1}var c=this;var m=setInterval(function(){if(obj_length(j)===0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var p=0;p<c.filters.length;p++){c.filters[p].update_ui_elt()}clearInterval(m)}},50)},delayed_draw:function(c,h,g,e,b,d,i,j,f){var a=setTimeout(function(){if(g<=c.view.high&&e>=c.view.low){var k=c.draw_tile(d,b,i,j);if(k){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(k).clone();var n=k.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,k);c.show_tile(k,i)}}delete f[a]},50);f[a]= true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(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($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.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;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g) {c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");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),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,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=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_conta iner);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={color:"black",min_value:undefined,max_value:undefined,mode:this.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));v ar d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.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){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,w=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(w)===undefined){this.get_data(o,r);return}var v=this.data_cache. get(w);if(!v){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(d-(h-k)/m*d);n.fillRect(u,h,f,d-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,d)}n.fill()}else{n.stroke()}c.append(b);return b},gen_options:funct ion(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetr ack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,e,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container,e);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.m ax_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,g,b,q){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=q;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,y=[],h=0,n=this.view.max_low;var A=[];if(this.inc_slots[a].mode!==q){delete this.inc_slots[a];this.inc_slots[a]={mode:q,w_scale:m};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var v=0,w=g.length;v<w;v++){var f=g[v],l=f[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);A.push(this.inc_slots[a][l])}else{y.push(v)}}for(var v=0,w =y.length;v<w;v++){var f=g[y[v]],l=f[0],r=f[1],c=f[2],p=f[3],d=Math.floor((r-n)*m),e=Math.ceil((c-n)*m);if(p!==undefined&&!b){var s=CONTEXT.measureText(p).width;if(d-s<0){e+=s}else{d-=s}}var u=0;while(u<=MAX_FEATURE_DEPTH){var o=true;if(this.s_e_by_tile[a][u]!==undefined){for(var t=0,z=this.s_e_by_tile[a][u].length;t<z;t++){var x=this.s_e_by_tile[a][u][t];if(e>x[0]&&d<x[1]){o=false;break}}}if(o){if(this.s_e_by_tile[a][u]===undefined){this.s_e_by_tile[a][u]=[]}this.s_e_by_tile[a][u].push([d,e]);this.inc_slots[a][l]=u;h=Math.max(h,u);break}u++}}return h},rect_or_text:function(r,l,t,b,q,f,i,e){r.textAlign="center";var k=0,p=Math.round(l/2);for(var m=0,s=i.length;m<s;m++){var j=i[m],d="MIDNSHP"[j[0]],n=j[1];if(d==="H"||d==="S"){k-=n}var g=q+k,w=Math.floor(Math.max(0,(g-t)*l)),h=Math.floor(Math.max(0,(g+n-t)*l));switch(d){case"S":case"H":case"M":var o=f.slice(k,n);if((this.mode==="Pack"||this.mode==="Auto")&&f!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillR ect(w+this.left_offset,e+1,h-w,9);r.fillStyle=CONNECTOR_COLOR;for(var u=0,a=o.length;u<a;u++){if(g+u>=t&&g+u<=b){var v=Math.floor(Math.max(0,(g+u-t)*l));r.fillText(o[u],v+this.left_offset+p,e+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(w+this.left_offset,e+4,h-w,3)}break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(w+this.left_offset,e+5,h-w,1);break;case"D":r.fillStyle="red";r.fillRect(w+this.left_offset,e+4,h-w,3);break;case"P":case"I":break}k+=n}},draw_tile:function(ag,o,s,av){var N=o*DENSITY*ag,al=(o+1)*DENSITY*ag,M=al-N;var an=(!this.initial_canvas?"initial":N+"_"+al);var I=this.data_cache.get(an);var e;if(I===undefined||(this.mode!=="Auto"&&I.dataset_type==="summary_tree")){this.data_queue[[N,al]]=true;this.get_data(N,al);return}var a=Math.ceil(M*av),ai=this.prefs.label_color,l=this.prefs.block_color,r=this.mode,z=25,ae=(r==="Squish")||(r==="Dense")&&(r!=="Pack")||(r==="Auto"&&(I.extra_info==="no_detail")),W=this.left_offset,au,D,aw;var q=document.createE lement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(q)}q=$(q);if(I.dataset_type==="summary_tree"){D=this.summary_draw_height}else{if(r==="Dense"){D=z;aw=10}else{aw=(ae?this.vertical_nodetail_px:this.vertical_detail_px);var A=(av<0.0001?1/this.view.zoom_res:av);D=this.incremental_slots(A,I.data,ae,r)*aw+z;au=this.inc_slots[A]}}q.css({position:"absolute",top:0,left:(N-this.view.low)*av-W});q.get(0).width=a+W;q.get(0).height=D;s.parent().css("height",Math.max(this.height_px,D)+"px");var J=q.get(0).getContext("2d");J.fillStyle=l;J.font=this.default_font;J.textAlign="right";this.container_div.find(".yaxislabel").remove();if(I.dataset_type=="summary_tree"){var Y=I.data,L=I.max,b=Math.ceil(I.delta*av);var p=$("<div />").addClass("yaxislabel").text(L);p.css({position:"absolute",top:"22px",left:"10px"});p.prependTo(this.container_div);for(var ap=0,H=Y.length;ap<H;ap++){var aa=Math.floor((Y[ap][0]-N)*av);var Z=Y[ap][1];if(!Z){continue}var am=Z/L*this.summary_ draw_height;J.fillStyle="black";J.fillRect(aa+W,this.summary_draw_height-am,b,am);if(this.prefs.show_counts&&J.measureText(Z).width<b){J.fillStyle="#bbb";J.textAlign="center";J.fillText(Z,aa+W+(b/2),this.summary_draw_height-5)}}e="Summary";s.append(q);return q}if(I.message){q.css({border:"solid red","border-width":"2px 2px 2px 0px"});J.fillStyle="red";J.textAlign="left";J.fillText(I.message,100+W,aw)}var ad=false;if(I.data){ad=true;for(var ar=0;ar<this.filters.length;ar++){if(!this.filters[ar].applies_to(I.data[0])){ad=false}}}if(ad){q.addClass(FILTERABLE_CLASS)}var at=I.data;var ao=0;for(var ap=0,H=at.length;ap<H;ap++){var S=at[ap],R=S[0],aq=S[1],ac=S[2],O=S[3];if(au[R]===undefined){continue}var ab=false;var U;for(var ar=0;ar<this.filters.length;ar++){U=this.filters[ar];U.update_attrs(S);if(!U.keep(S)){ab=true;break}}if(ab){continue}if(aq<=al&&ac>=N){var af=Math.floor(Math.max(0,(aq-N)*av)),K=Math.ceil(Math.min(a,Math.max(0,(ac-N)*av))),X=(r==="Dense"?1:(1+au[R]))*aw;var G, aj,P=null,ax=null;if(I.dataset_type==="bai"){var v=S[4];J.fillStyle=l;if(S[5] instanceof Array){var E=Math.floor(Math.max(0,(S[5][0]-N)*av)),Q=Math.ceil(Math.min(a,Math.max(0,(S[5][1]-N)*av))),C=Math.floor(Math.max(0,(S[6][0]-N)*av)),w=Math.ceil(Math.min(a,Math.max(0,(S[6][1]-N)*av)));if(S[5][1]>=N&&S[5][0]<=al){this.rect_or_text(J,av,N,al,S[5][0],S[5][2],v,X)}if(S[6][1]>=N&&S[6][0]<=al){this.rect_or_text(J,av,N,al,S[6][0],S[6][2],v,X)}if(C>Q){J.fillStyle=CONNECTOR_COLOR;J.fillRect(Q+W,X+5,C-Q,1)}}else{J.fillStyle=l;this.rect_or_text(J,av,N,al,aq,O,v,X)}if(r!=="Dense"&&!ae&&aq>N){J.fillStyle=this.prefs.label_color;if(o===0&&af-J.measureText(O).width<0){J.textAlign="left";J.fillText(R,K+2+W,X+8)}else{J.textAlign="right";J.fillText(R,af-2+W,X+8)}J.fillStyle=l}}else{if(I.dataset_type==="interval_index"){if(ae){J.fillStyle=l;J.fillRect(af+W,X+5,K-af,1)}else{var F=S[4],V=S[5],ah=S[6],h=S[7];if(V&&ah){P=Math.floor(Math.max(0,(V-N)*av));ax=Math.ceil(Math.min(a,Math.max(0,(ah-N)*av) ))}if(r!=="Dense"&&O!==undefined&&aq>N){J.fillStyle=ai;if(o===0&&af-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+W,X+8)}else{J.textAlign="right";J.fillText(O,af-2+W,X+8)}J.fillStyle=l}if(h){if(F){if(F=="+"){J.fillStyle=RIGHT_STRAND}else{if(F=="-"){J.fillStyle=LEFT_STRAND}}J.fillRect(af+W,X,K-af,10);J.fillStyle=l}for(var an=0,g=h.length;an<g;an++){var u=h[an],d=Math.floor(Math.max(0,(u[0]-N)*av)),T=Math.ceil(Math.min(a,Math.max((u[1]-N)*av)));if(d>T){continue}G=5;aj=3;J.fillRect(d+W,X+aj,T-d,G);if(P!==undefined&&!(d>ax||T<P)){G=9;aj=1;var ak=Math.max(d,P),B=Math.min(T,ax);J.fillRect(ak+W,X+aj,B-ak,G)}}}else{G=9;aj=1;J.fillRect(af+W,X+aj,K-af,G);if(S.strand){if(S.strand=="+"){J.fillStyle=RIGHT_STRAND_INV}else{if(S.strand=="-"){J.fillStyle=LEFT_STRAND_INV}}J.fillRect(af+W,X,K-af,10);J.fillStyle=l}}}}else{if(I.dataset_type==="vcf"){if(ae){J.fillStyle=l;J.fillRect(af+W,X+5,K-af,1)}else{var t=S[4],n=S[5],c=S[6];G=9;aj=1;J.fillRect(af+W,X,K-af,G);if(r!=="Dense"&&O! ==undefined&&aq>N){J.fillStyle=ai;if(o===0&&af-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+W,X+8)}else{J.textAlign="right";J.fillText(O,af-2+W,X+8)}J.fillStyle=l}var m=t+" / "+n;if(aq>N&&J.measureText(m).width<(K-af)){J.fillStyle="white";J.textAlign="center";J.fillText(m,W+af+(K-af)/2,X+8);J.fillStyle=l}}}}}ao++}}return q},gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_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=$("<div />").append(b).append(c);return a.append(k).append( l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,e,c){FeatureTrack.call(this,d,b,a,e,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 ef3e52251722: Merge
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 Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1289493322 18000 # Node ID ef3e52251722c1086160643a5f700c5db75a71d4 # Parent 865d7175847ad322959f6b85532357d0f69afa46 # Parent 7ea4c156ae32c4757378229bfc49584df91a024a Merge

1 0

galaxy-dist commit 591c53b44ae4: Fixes for links that direct admin and regular users to different views of selected or transferred sample dataset files.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1289487850 18000 # Node ID 591c53b44ae4a6237a841adaa3abfe59829beebe # Parent bbc0f56e3e16f93bf3c81d09b0fa12876a3f2579 Fixes for links that direct admin and regular users to different views of selected or transferred sample dataset files. --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -125,7 +125,7 @@ can_delete_samples = not is_complete display_checkboxes = editing_samples and ( is_complete or is_rejected or is_submitted ) display_bar_code = request.samples and ( is_complete or is_rejected or is_submitted ) - display_datasets = request.samples and ( is_complete or is_rejected or is_submitted ) + display_datasets = request.samples and ( is_complete or is_submitted ) else: is_complete = False is_submitted = False @@ -175,33 +175,44 @@ <td valign="top"> ## An admin can select the datasets to transfer, while a non-admin can only view what has been selected %if is_admin: - <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a> + ## This link will direct the admin to a page allowing them to select datasets. + <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id= trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a> %elif sample.datasets: - ## Only display a link if there is at least 1 selected dataset for the sample - <a href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a></td> + ## Since this is a regular user, only display a link if there is at least 1 + ## selected dataset for the sample. + <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a> %else: + ## Since this is a regular user, do not display a link if there are no datasets. ${len( sample.datasets )} %endif </td><td valign="top"> %if is_admin: - %if sample.untransferred_dataset_files: + <% + if sample.transferred_dataset_files: + transferred_dataset_files = sample.transferred_dataset_files + else: + transferred_dataset_files = [] + %> + %if not sample.datasets: + ## No datasets have been selected for this sample, so don't include a link + ${len( sample.transferred_dataset_files )} + %elif len( sample.datasets ) > len( transferred_dataset_files ): ## At least 1 selected dataset is not yet transferred, so this link ## will direct the admin to a page allowing them to transfer datasets. - <a href="${h.url_for( controller='requests_common', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.transferred_dataset_files )}</a> - %else: + <a href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.transferred_dataset_files )}</a> + %elif len( sample.datasets ) == len( transferred_dataset_files ): ## All selected datasets have successfully transferred, so this link ## will direct the admin to a page displaying all transferred datasets. <a href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ), transfer_status=trans.model.SampleDataset.transfer_status.COMPLETE )}">${len( sample.transferred_dataset_files )}</a> %endif %else: %if sample.transferred_dataset_files: - ## The cuurent user is not an admin, so this link will direct the - ## user to the target data library containing those datasets that - ## were successfully transferred. + ## Since this is a regular user, this link will direct them to the target + ## data library containing those datasets that were successfully transferred. <a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( sample.library.id ) )}">${len( sample.transferred_dataset_files )}</a> %else: - ## Display a 0 with no link. + ## Since this is a regular user, do not display a link. ${len( sample.transferred_dataset_files )} %endif %endif @@ -228,7 +239,7 @@ can_select_datasets = is_admin and current_samples and ( is_submitted or is_complete ) display_checkboxes = editing_samples and ( is_complete or is_rejected or is_submitted ) display_bar_code = request.samples and ( is_complete or is_rejected or is_submitted ) - display_datasets = request.samples and ( is_complete or is_rejected or is_submitted ) + display_datasets = request.samples and ( is_complete or is_submitted ) %> ${grid_header} %if render_buttons and ( can_add_samples or can_edit_samples ): @@ -314,39 +325,44 @@ <td> ## An admin can select the datasets to transfer, while a non-admin can only view what has been selected %if is_admin: - %if not sample.datasets: - ## If there are no selected datasets, display a page alowing the admin to select some. - <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id= trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a> - %else: - ## If there are selected datasets, display them - <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a> - %endif + ## This link will direct the admin to a page allowing them to select datasets. + <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id= trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a> %elif sample.datasets: - ## Only display a link if there is at least 1 selected dataset for the sample + ## Since this is a regular user, only display a link if there is at least 1 + ## selected dataset for the sample. <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a> %else: + ## Since this is a regular user, do not display a link if there are no datasets. ${len( sample.datasets )} %endif </td><td> %if is_admin: - %if sample.untransferred_dataset_files: + <% + if sample.transferred_dataset_files: + transferred_dataset_files = sample.transferred_dataset_files + else: + transferred_dataset_files = [] + %> + %if not sample.datasets: + ## No datasets have been selected for this sample, so don't include a link + ${len( sample.transferred_dataset_files )} + %elif len( sample.datasets ) > len( transferred_dataset_files ): ## At least 1 selected dataset is not yet transferred, so this link ## will direct the admin to a page allowing them to transfer datasets. - <a href="${h.url_for( controller='requests_common', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.transferred_dataset_files )}</a> - %else: + <a href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.transferred_dataset_files )}</a> + %elif len( sample.datasets ) == len( transferred_dataset_files ): ## All selected datasets have successfully transferred, so this link ## will direct the admin to a page displaying all transferred datasets. <a href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ), transfer_status=trans.model.SampleDataset.transfer_status.COMPLETE )}">${len( sample.transferred_dataset_files )}</a> %endif %else: %if sample.transferred_dataset_files: - ## The cuurent user is not an admin, so this link will direct the - ## user to the target data library containing those datasets that - ## were successfully transferred. + ## Since this is a regular user, this link will direct them to the target + ## data library containing those datasets that were successfully transferred. <a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( sample.library.id ) )}">${len( sample.transferred_dataset_files )}</a> %else: - ## Display a 0 with no link. + ## Since this is a regular user, do not display a link. ${len( sample.transferred_dataset_files )} %endif %endif --- a/templates/requests/common/view_sample_datasets.mako +++ b/templates/requests/common/view_sample_datasets.mako @@ -37,7 +37,7 @@ ${render_sample_datasets( cntrller, sample, sample_datasets, title )} %else: %if transfer_status: - No datasets with status ${transfer_status}" belong to this sample + No datasets with status "${transfer_status}" belong to this sample %else: No datasets have been selected for this sample. %endif

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galaxy-dist commit d56f296aaa61: Minimally functional splitting.
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 Dannon Baker <dannonbaker(a)me.com> # Date 1289408765 18000 # Node ID d56f296aaa610a537d35cb7d235eac9d8f596464 # Parent d6a0dd8e55e2f7d2077bc282bca3e42d98fbb7f2 Minimally functional splitting. Disabled by default, not advisable to enable on a production server (or main!) until scheduling issues are looked at and performance analysis has been done. Tested 'basic' splitting with many basic tools (bowtie, bwa, filter sam, others). This style of splitting should work for most 'embarassingly parallel' one input, one output tools (no dependence between parallel tasks). --- a/tools/sr_mapping/bowtie_wrapper.xml +++ b/tools/sr_mapping/bowtie_wrapper.xml @@ -1,6 +1,7 @@ <tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.0"><requirements><requirement type='package'>bowtie</requirement></requirements><description></description> + <parallelism method="basic"></parallelism><command interpreter="python"> bowtie_wrapper.py --threads="4" --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1,10 +1,11 @@ -import logging, threading, sys, os, time, subprocess, string, tempfile, re, traceback, shutil +import logging, threading, sys, os, time, traceback, shutil import galaxy from galaxy import util, model from galaxy.model.orm import lazyload from galaxy.datatypes.tabular import * from galaxy.datatypes.interval import * +# tabular/interval imports appear to be unused. Clean up? from galaxy.datatypes import metadata from galaxy.util.json import from_json_string from galaxy.util.expressions import ExpressionContext @@ -13,8 +14,6 @@ from galaxy.jobs.actions.post import Act import pkg_resources pkg_resources.require( "PasteDeploy" ) -from paste.deploy.converters import asbool - from Queue import Queue, Empty log = logging.getLogger( __name__ ) @@ -83,11 +82,9 @@ class JobQueue( object ): self.parent_pid = os.getpid() # Contains new jobs. Note this is not used if track_jobs_in_database is True self.queue = Queue() - # Contains jobs that are waiting (only use from monitor thread) ## This and jobs_to_check[] are closest to a "Job Queue" self.waiting_jobs = [] - # Helper for interruptable sleep self.sleeper = Sleeper() self.running = True @@ -104,7 +101,7 @@ class JobQueue( object ): the database and requeues or cleans up as necessary. Only run as the job manager starts. """ - model = self.app.model + model = self.app.model # DBTODO Why? for job in self.sa_session.query( model.Job ).filter( model.Job.state == model.Job.states.NEW ): if job.tool_id not in self.app.toolbox.tools_by_id: log.warning( "Tool '%s' removed from tool config, unable to recover job: %s" % ( job.tool_id, job.id ) ) @@ -294,7 +291,10 @@ class JobWrapper( object ): self.tool_provided_job_metadata = None # Wrapper holding the info required to restore and clean up from files used for setting metadata externally self.external_output_metadata = metadata.JobExternalOutputMetadataWrapper( job ) - + + def get_job( self ): + return self.sa_session.query( model.Job ).get( self.job_id ) + def get_param_dict( self ): """ Restore the dictionary of parameters from the database. @@ -479,9 +479,9 @@ class JobWrapper( object ): self.fail( job.info ) return if stderr: - job.state = "error" + job.state = job.states.ERROR else: - job.state = 'ok' + job.state = job.states.OK if self.app.config.outputs_to_working_directory: for dataset_path in self.get_output_fnames(): try: @@ -761,6 +761,215 @@ class JobWrapper( object ): else: return 'anonymous@unknown' +class TaskWrapper(JobWrapper): + """ + Extension of JobWrapper intended for running tasks. + Should be refactored into a generalized executable unit wrapper parent, then jobs and tasks. + """ + # Abstract this to be more useful for running tasks that *don't* necessarily compose a job. + + def __init__(self, task, queue): + super(TaskWrapper, self).__init__(task.job, queue) + self.task_id = task.id + self.parallelism = None + if task.part_file: + #do this better + self.working_directory = os.path.dirname(task.part_file) + else: + self.working_directory = None + self.status = task.states.NEW + + def get_job( self ): + if self.job_id: + return self.sa_session.query( model.Job ).get( self.job_id ) + else: + return None + + def get_task( self ): + return self.sa_session.query(model.Task).get(self.task_id) + + def get_param_dict( self ): + """ + Restore the dictionary of parameters from the database. + """ + job = self.sa_session.query( model.Job ).get( self.job_id ) + param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] ) + param_dict = self.tool.params_from_strings( param_dict, self.app ) + return param_dict + + def prepare( self ): + """ + Prepare the job to run by creating the working directory and the + config files. + """ + # Restore parameters from the database + job = self.get_job() + task = self.get_task() + if job.user is None and job.galaxy_session is None: + raise Exception( 'Job %s has no user and no session.' % job.id ) + incoming = dict( [ ( p.name, p.value ) for p in job.parameters ] ) + incoming = self.tool.params_from_strings( incoming, self.app ) + # Do any validation that could not be done at job creation + self.tool.handle_unvalidated_param_values( incoming, self.app ) + # Restore input / output data lists + inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) + # DBTODO New method for generating command line for a task? + out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) + out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] ) + # These can be passed on the command line if wanted as $userId $userEmail + if job.history and job.history.user: # check for anonymous user! + userId = '%d' % job.history.user.id + userEmail = str(job.history.user.email) + else: + userId = 'Anonymous' + userEmail = 'Anonymous' + incoming['userId'] = userId + incoming['userEmail'] = userEmail + # Build params, done before hook so hook can use + param_dict = self.tool.build_param_dict( incoming, inp_data, out_data, self.get_output_fnames(), self.working_directory ) + fnames = {} + for v in self.get_input_fnames(): + fnames[v] = os.path.join(self.working_directory, os.path.basename(v)) + for dp in [x.real_path for x in self.get_output_fnames()]: + fnames[dp] = os.path.join(self.working_directory, os.path.basename(dp)) + # Certain tools require tasks to be completed prior to job execution + # ( this used to be performed in the "exec_before_job" hook, but hooks are deprecated ). + self.tool.exec_before_job( self.queue.app, inp_data, out_data, param_dict ) + # Run the before queue ("exec_before_job") hook + self.tool.call_hook( 'exec_before_job', self.queue.app, inp_data=inp_data, + out_data=out_data, tool=self.tool, param_dict=incoming) + self.sa_session.flush() + # Build any required config files + config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) + # FIXME: Build the param file (might return None, DEPRECATED) + param_filename = self.tool.build_param_file( param_dict, self.working_directory ) + # Build the job's command line + self.command_line = self.tool.build_command_line( param_dict ) + # HACK, Fix this when refactored. + for k, v in fnames.iteritems(): + self.command_line = self.command_line.replace(k, v) + # FIXME: for now, tools get Galaxy's lib dir in their path + if self.command_line and self.command_line.startswith( 'python' ): + self.galaxy_lib_dir = os.path.abspath( "lib" ) # cwd = galaxy root + # Shell fragment to inject dependencies + if self.app.config.use_tool_dependencies: + self.dependency_shell_commands = self.tool.build_dependency_shell_commands() + else: + self.dependency_shell_commands = None + # We need command_line persisted to the db in order for Galaxy to re-queue the job + # if the server was stopped and restarted before the job finished + task.command_line = self.command_line + self.sa_session.add( task ) + self.sa_session.flush() + # # Return list of all extra files + extra_filenames = config_filenames + if param_filename is not None: + extra_filenames.append( param_filename ) + self.param_dict = param_dict + self.extra_filenames = extra_filenames + self.status = 'prepared' + return extra_filenames + + def fail( self, message, exception=False ): + log.error("TaskWrapper Failure %s" % message) + self.status = 'error' + # How do we want to handle task failure? Fail the job and let it clean up? + + def change_state( self, state, info = False ): + task = self.get_task() + self.sa_session.refresh( task ) + if info: + task.info = info + task.state = state + self.sa_session.add( task ) + self.sa_session.flush() + + def get_state( self ): + task = self.get_task() + self.sa_session.refresh( task ) + return task.state + + def set_runner( self, runner_url, external_id ): + task = self.get_task() + self.sa_session.refresh( task ) + task.task_runner_name = runner_url + task.task_runner_external_id = external_id + # DBTODO Check task job_runner_stuff + self.sa_session.add( task ) + self.sa_session.flush() + + def finish( self, stdout, stderr ): + # DBTODO integrate previous finish logic. + # Simple finish for tasks. Just set the flag OK. + log.debug( 'task %s for job %d ended' % (self.task_id, self.job_id) ) + """ + Called to indicate that the associated command has been run. Updates + the output datasets based on stderr and stdout from the command, and + the contents of the output files. + """ + # default post job setup_external_metadata + self.sa_session.expunge_all() + task = self.get_task() + # if the job was deleted, don't finish it + if task.state == task.states.DELETED: + self.cleanup() + return + elif task.state == task.states.ERROR: + # Job was deleted by an administrator + self.fail( task.info ) + return + if stderr: + task.state = task.states.ERROR + else: + task.state = task.states.OK + # Save stdout and stderr + if len( stdout ) > 32768: + log.error( "stdout for task %d is greater than 32K, only first part will be logged to database" % task.id ) + task.stdout = stdout[:32768] + if len( stderr ) > 32768: + log.error( "stderr for job %d is greater than 32K, only first part will be logged to database" % task.id ) + task.stderr = stderr[:32768] + task.command_line = self.command_line + self.sa_session.flush() + log.debug( 'task %d ended' % self.task_id ) + + def cleanup( self ): + # There is no task cleanup. The job cleans up for all tasks. + pass + + def get_command_line( self ): + return self.command_line + + def get_session_id( self ): + return self.session_id + + def get_output_file_id( self, file ): + # There is no permanent output file for tasks. + return None + + def get_tool_provided_job_metadata( self ): + # DBTODO Handle this as applicable for tasks. + return None + + def get_dataset_finish_context( self, job_context, dataset ): + # Handled at the parent job level. Do nothing here. + pass + + def check_output_sizes( self ): + sizes = [] + output_paths = self.get_output_fnames() + for outfile in [ str( o ) for o in output_paths ]: + sizes.append( ( outfile, os.stat( outfile ).st_size ) ) + return sizes + + def setup_external_metadata( self, exec_dir = None, tmp_dir = None, dataset_files_path = None, config_root = None, datatypes_config = None, set_extension = True, **kwds ): + # There is no metadata setting for tasks. This is handled after the merge, at the job level. + pass + + @property + def user( self ): + pass + class DefaultJobDispatcher( object ): def __init__( self, app ): self.app = app @@ -768,10 +977,15 @@ class DefaultJobDispatcher( object ): start_job_runners = ["local"] if app.config.start_job_runners is not None: start_job_runners.extend( app.config.start_job_runners.split(",") ) + if app.config.use_tasked_jobs: + start_job_runners.append("tasks") for runner_name in start_job_runners: if runner_name == "local": import runners.local self.job_runners[runner_name] = runners.local.LocalJobRunner( app ) + elif runner_name == "tasks": + import runners.tasks + self.job_runners[runner_name] = runners.tasks.TaskedJobRunner( app ) elif runner_name == "pbs": import runners.pbs self.job_runners[runner_name] = runners.pbs.PBSJobRunner( app ) @@ -782,12 +996,17 @@ class DefaultJobDispatcher( object ): import runners.drmaa self.job_runners[runner_name] = runners.drmaa.DRMAAJobRunner( app ) else: - log.error( "Unable to start unknown job runner: %s" %runner_name ) + log.error( "Unable to start unknown job runner: '%s'" %runner_name ) def put( self, job_wrapper ): - runner_name = ( job_wrapper.tool.job_runner.split(":", 1) )[0] - log.debug( "dispatching job %d to %s runner" %( job_wrapper.job_id, runner_name ) ) - self.job_runners[runner_name].put( job_wrapper ) + if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None and not isinstance(job_wrapper, TaskWrapper): + runner_name = "tasks" + log.debug( "dispatching job %d to %s runner" %( job_wrapper.job_id, runner_name ) ) + self.job_runners[runner_name].put( job_wrapper ) + else: + runner_name = ( job_wrapper.tool.job_runner.split(":", 1) )[0] + log.debug( "dispatching job %d to %s runner" %( job_wrapper.job_id, runner_name ) ) + self.job_runners[runner_name].put( job_wrapper ) def stop( self, job ): runner_name = ( job.job_runner_name.split(":", 1) )[0] --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -176,6 +176,44 @@ class Job( object ): dataset.peek = 'Job deleted' dataset.info = 'Job output deleted by user before job completed' +class Task( object ): + """ + A task represents a single component of a job. + """ + states = Bunch( NEW = 'new', + WAITING = 'waiting', + QUEUED = 'queued', + RUNNING = 'running', + OK = 'ok', + ERROR = 'error', + DELETED = 'deleted' ) + + def __init__( self, job, part_file = None ): + self.command_line = None + self.parameters = [] + self.state = Task.states.NEW + self.info = None + self.part_file = part_file + self.task_runner_name = None + self.task_runner_external_id = None + self.job = job + self.stdout = None + self.stderr = None + + def set_state( self, state ): + self.state = state + + def get_param_values( self, app ): + """ + Read encoded parameter values from the database and turn back into a + dict of tool parameter values. + """ + param_dict = dict( [ ( p.name, p.value ) for p in self.parent_job.parameters ] ) + tool = app.toolbox.tools_by_id[self.tool_id] + param_dict = tool.params_from_strings( param_dict, app ) + return param_dict + + class JobParameter( object ): def __init__( self, name, value ): self.name = name --- a/tools/samtools/sam_bitwise_flag_filter.xml +++ b/tools/samtools/sam_bitwise_flag_filter.xml @@ -1,5 +1,6 @@ <tool id="sam_bw_filter" name="Filter SAM" version="1.0.0"><description>on bitwise flag values</description> + <parallelism method="basic"></parallelism><command interpreter="python"> sam_bitwise_flag_filter.py --input_sam_file=$input1 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -367,7 +367,12 @@ class Tool: self.redirect_url_params = '' # Short description of the tool self.description = util.xml_text(root, "description") - # Job runner + # Parallelism for tasks, read from tool config. + parallelism = root.find("parallelism") + if parallelism is not None and parallelism.get("method"): + self.parallelism = parallelism.get("method") + else: + self.parallelism = None if self.app.config.start_job_runners is None: # Jobs are always local regardless of tool config if no additional # runners are started --- a/tools/sr_mapping/bwa_wrapper.xml +++ b/tools/sr_mapping/bwa_wrapper.xml @@ -1,5 +1,6 @@ <tool id="bwa_wrapper" name="Map with BWA" version="1.1.0"><description></description> + <parallelism method="basic"></parallelism><command interpreter="python"> bwa_wrapper.py --threads="4" --- /dev/null +++ b/lib/galaxy/jobs/runners/tasks.py @@ -0,0 +1,206 @@ +import logging +import subprocess +from Queue import Queue +import threading + +from galaxy import model + +import os, errno +from time import sleep + +from galaxy.jobs import TaskWrapper + +log = logging.getLogger( __name__ ) + +class TaskedJobRunner( object ): + """ + Job runner backed by a finite pool of worker threads. FIFO scheduling + """ + STOP_SIGNAL = object() + def __init__( self, app ): + """Start the job runner with 'nworkers' worker threads""" + self.app = app + self.sa_session = app.model.context + # start workers + self.queue = Queue() + self.threads = [] + nworkers = app.config.local_task_queue_workers + log.info( "Starting tasked-job runners" ) + for i in range( nworkers ): + worker = threading.Thread( target=self.run_next ) + worker.start() + self.threads.append( worker ) + log.debug( "%d workers ready", nworkers ) + + def run_next( self ): + """Run the next job, waiting until one is available if neccesary""" + while 1: + job_wrapper = self.queue.get() + if job_wrapper is self.STOP_SIGNAL: + return + try: + self.run_job( job_wrapper ) + except: + log.exception( "Uncaught exception running tasked job" ) + + def run_job( self, job_wrapper ): + job_wrapper.set_runner( 'tasks:///', None ) + stderr = stdout = command_line = '' + # Prepare the job to run + try: + job_wrapper.prepare() + command_line = job_wrapper.get_command_line() + except: + job_wrapper.fail( "failure preparing job", exception=True ) + log.exception("failure running job %d" % job_wrapper.job_id) + return + # If we were able to get a command line, run the job. ( must be passed to tasks ) + if command_line: + try: + # DBTODO read tool info and use the right kind of parallelism. + # For now, the only splitter is the 'basic' one, n-ways split on one input, one output. + # This is incredibly simplified. Parallelism ultimately needs to describe which inputs, how, etc. + job_wrapper.change_state( model.Job.states.RUNNING ) + self.sa_session.flush() + parent_job = job_wrapper.get_job() + # Split with the tool-defined method. + if job_wrapper.tool.parallelism == "basic": + from galaxy.jobs.splitters import basic + if len(job_wrapper.get_input_fnames()) > 1 or len(job_wrapper.get_output_fnames()) > 1: + log.error("The basic splitter is not capable of handling jobs with multiple inputs or outputs.") + job_wrapper.change_state( model.Job.states.ERROR ) + job_wrapper.fail("Job Splitting Failed, the basic splitter only handles tools with one input and one output") + # Requeue as a standard job? + return + input_file = job_wrapper.get_input_fnames()[0] + working_directory = job_wrapper.working_directory + # DBTODO execute an external task to do the splitting, this should happen at refactor. + # Regarding number of ways split, use "hints" in tool config? + # If the number of tasks is sufficiently high, we can use it to calculate job completion % and give a running status. + basic.split(input_file, working_directory, + 20, #Needs serious experimentation to find out what makes the most sense. + parent_job.input_datasets[0].dataset.ext) + # Tasks in this parts list are in alphabetical listdir order (15 before 5), but that should not matter. + parts = [os.path.join(os.path.abspath(job_wrapper.working_directory), p, os.path.basename(input_file)) + for p in os.listdir(job_wrapper.working_directory) + if p.startswith('task_')] + else: + job_wrapper.change_state( model.Job.states.ERROR ) + job_wrapper.fail("Job Splitting Failed, no match for '%s'" % job_wrapper.tool.parallelism) + # Assemble parts into task_wrappers + + # Not an option for now. Task objects don't *do* anything useful yet, but we'll want them tracked outside this thread to do anything. + # if track_tasks_in_database: + tasks = [] + task_wrappers = [] + for part in parts: + task = model.Task(parent_job, part) + self.sa_session.add(task) + tasks.append(task) + self.sa_session.flush() + # Must flush prior to the creation and queueing of task wrappers. + for task in tasks: + tw = TaskWrapper(task, job_wrapper.queue) + task_wrappers.append(tw) + self.app.job_manager.dispatcher.put(tw) + tasks_incomplete = False + sleep_time = 1 + while tasks_incomplete is False: + tasks_incomplete = True + for tw in task_wrappers: + if not tw.get_state() == model.Task.states.OK: + tasks_incomplete = False + sleep( sleep_time ) + if sleep_time < 8: + sleep_time *= 2 + output_filename = job_wrapper.get_output_fnames()[0].real_path + basic.merge(working_directory, output_filename) + log.debug('execution finished: %s' % command_line) + for tw in task_wrappers: + stdout += tw.get_task().stdout + stderr += tw.get_task().stderr + except Exception: + job_wrapper.fail( "failure running job", exception=True ) + log.exception("failure running job %d" % job_wrapper.job_id) + return + + #run the metadata setting script here + #this is terminate-able when output dataset/job is deleted + #so that long running set_meta()s can be canceled without having to reboot the server + if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] and self.app.config.set_metadata_externally and job_wrapper.output_paths: + external_metadata_script = job_wrapper.setup_external_metadata( output_fnames = job_wrapper.get_output_fnames(), + set_extension = True, + kwds = { 'overwrite' : False } ) #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior + log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) + external_metadata_proc = subprocess.Popen( args = external_metadata_script, + shell = True, + env = os.environ, + preexec_fn = os.setpgrp ) + job_wrapper.external_output_metadata.set_job_runner_external_pid( external_metadata_proc.pid, self.sa_session ) + external_metadata_proc.wait() + log.debug( 'execution of external set_meta finished for job %d' % job_wrapper.job_id ) + + # Finish the job + try: + job_wrapper.finish( stdout, stderr ) + except: + log.exception("Job wrapper finish method failed") + job_wrapper.fail("Unable to finish job", exception=True) + + def put( self, job_wrapper ): + """Add a job to the queue (by job identifier)""" + # Change to queued state before handing to worker thread so the runner won't pick it up again + job_wrapper.change_state( model.Job.states.QUEUED ) + self.queue.put( job_wrapper ) + + def shutdown( self ): + """Attempts to gracefully shut down the worker threads""" + log.info( "sending stop signal to worker threads" ) + for i in range( len( self.threads ) ): + self.queue.put( self.STOP_SIGNAL ) + log.info( "local job runner stopped" ) + + def check_pid( self, pid ): + # DBTODO Need to check all subtask pids and return some sort of cumulative result. + return True + try: + os.kill( pid, 0 ) + return True + except OSError, e: + if e.errno == errno.ESRCH: + log.debug( "check_pid(): PID %d is dead" % pid ) + else: + log.warning( "check_pid(): Got errno %s when attempting to check PID %d: %s" %( errno.errorcode[e.errno], pid, e.strerror ) ) + return False + + def stop_job( self, job ): + # DBTODO Call stop on all of the tasks. + #if our local job has JobExternalOutputMetadata associated, then our primary job has to have already finished + if job.external_output_metadata: + pid = job.external_output_metadata[0].job_runner_external_pid #every JobExternalOutputMetadata has a pid set, we just need to take from one of them + else: + pid = job.job_runner_external_id + if pid in [ None, '' ]: + log.warning( "stop_job(): %s: no PID in database for job, unable to stop" % job.id ) + return + pid = int( pid ) + if not self.check_pid( pid ): + log.warning( "stop_job(): %s: PID %d was already dead or can't be signaled" % ( job.id, pid ) ) + return + for sig in [ 15, 9 ]: + try: + os.killpg( pid, sig ) + except OSError, e: + log.warning( "stop_job(): %s: Got errno %s when attempting to signal %d to PID %d: %s" % ( job.id, errno.errorcode[e.errno], sig, pid, e.strerror ) ) + return # give up + sleep( 2 ) + if not self.check_pid( pid ): + log.debug( "stop_job(): %s: PID %d successfully killed with signal %d" %( job.id, pid, sig ) ) + return + else: + log.warning( "stop_job(): %s: PID %d refuses to die after signaling TERM/KILL" %( job.id, pid ) ) + + def recover( self, job, job_wrapper ): + # DBTODO Task Recovery, this should be possible. + job_wrapper.change_state( model.Job.states.ERROR, info = "This job was killed when Galaxy was restarted. Please retry the job." ) + --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -347,6 +347,11 @@ use_interactive = True # Necessary if you're running the load balanced setup. #track_jobs_in_database = False +# This enables splitting of jobs into tasks, if specified by the particular tool config. +# This is a new feature and not recommended for production servers yet. +#use_tasked_jobs = True +#local_task_queue_workers = 2 + # Enable job recovery (if Galaxy is restarted while cluster jobs are running, # it can "recover" them when it starts). This is not safe to use if you are # running more than one Galaxy server using the same database. --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -391,7 +391,24 @@ JobImportHistoryArchive.table = Table( " Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), Column( "archive_dir", TEXT ) ) - + +Task.table = Table( "task", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "execution_time", DateTime ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "state", String( 64 ), index=True ), + Column( "command_line", TEXT ), + Column( "param_filename", String( 1024 ) ), + Column( "runner_name", String( 255 ) ), + Column( "stdout", TEXT ), + Column( "stderr", TEXT ), + Column( "traceback", TEXT ), + Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=False ), + Column( "part_file", String(1024)), + Column( "task_runner_name", String( 255 ) ), + Column( "task_runner_external_id", String( 255 ) ) ) + PostJobAction.table = Table("post_job_action", metadata, Column("id", Integer, primary_key=True), Column("workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False), @@ -1251,6 +1268,10 @@ assign_mapper( context, Job, Job.table, output_library_datasets=relation( JobToOutputLibraryDatasetAssociation, lazy=False ), external_output_metadata = relation( JobExternalOutputMetadata, lazy = False ) ) ) +assign_mapper( context, Task, Task.table, + properties=dict( job = relation( Job ))) + + assign_mapper( context, Event, Event.table, properties=dict( history=relation( History ), galaxy_session=relation( GalaxySession ), --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -4,7 +4,6 @@ Universe configuration builder. import sys, os import logging, logging.config -from optparse import OptionParser import ConfigParser from galaxy.util import string_as_bool @@ -76,6 +75,9 @@ class Configuration( object ): self.error_email_to = kwargs.get( 'error_email_to', None ) self.smtp_server = kwargs.get( 'smtp_server', None ) self.start_job_runners = kwargs.get( 'start_job_runners', None ) + # Tasked job runner. + self.use_tasked_jobs = string_as_bool( kwargs.get( 'use_tasked_jobs', False ) ) + self.local_task_queue_workers = int(kwargs.get("local_task_queue_workers", 2)) self.default_cluster_job_runner = kwargs.get( 'default_cluster_job_runner', 'local:///' ) self.pbs_application_server = kwargs.get('pbs_application_server', "" ) self.pbs_dataset_server = kwargs.get('pbs_dataset_server', "" ) --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0061_tasks.py @@ -0,0 +1,49 @@ +""" +Migration script to create tables task management. +""" +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) +now = datetime.datetime.utcnow + +Task_table = Table( "task", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "execution_time", DateTime ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "state", String( 64 ), index=True ), + Column( "command_line", TEXT ), + Column( "param_filename", String( 1024 ) ), + Column( "runner_name", String( 255 ) ), + Column( "stdout", TEXT ), + Column( "stderr", TEXT ), + Column( "traceback", TEXT ), + Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=False ), + Column( "part_file", String(1024)), + Column( "task_runner_name", String( 255 ) ), + Column( "task_runner_external_id", String( 255 ) ) ) + +tables = [Task_table] + +def upgrade(): + print __doc__ + metadata.reflect() + for table in tables: + try: + table.create() + except: + log.warn( "Failed to create table '%s', ignoring (might result in wrong schema)" % table.name ) + +def downgrade(): + metadata.reflect() + for table in tables: + table.drop() --- /dev/null +++ b/lib/galaxy/jobs/splitters/basic.py @@ -0,0 +1,85 @@ +import os, logging +log = logging.getLogger( __name__ ) + +def _file_len(fname): + i = 0 + with open(fname) as f: + for i, l in enumerate(f): + pass + return i + 1 + +def _fq_seq_count(fname): + count = 0 + with open(fname) as f: + for i, l in enumerate(f): + if l.startswith('@'): + count += 1 + return count + +def split_fq(input_file, working_directory, parts): + # Temporary, switch this to use the fq reader in lib/galaxy_utils/sequence. + outputs = [] + length = _fq_seq_count(input_file) + if length < 1: + return outputs + if length < parts: + parts = length + len_each, remainder = divmod(length, parts) + with open(input_file, 'rt') as f: + for p in range(0, parts): + part_dir = os.path.join( os.path.abspath(working_directory), 'task_%s' % p) + if not os.path.exists( part_dir ): + os.mkdir( part_dir ) + part_path = os.path.join(part_dir, os.path.basename(input_file)) + with open(part_path, 'w') as part_file: + for l in range(0, len_each): + part_file.write(f.readline()) + part_file.write(f.readline()) + part_file.write(f.readline()) + part_file.write(f.readline()) + if remainder > 0: + part_file.write(f.readline()) + part_file.write(f.readline()) + part_file.write(f.readline()) + part_file.write(f.readline()) + remainder -= 1 + outputs.append(part_path) + return outputs + +def split_txt(input_file, working_directory, parts): + outputs = [] + length = _file_len(input_file) + if length < parts: + parts = length + len_each, remainder = divmod(length, parts) + with open(input_file, 'rt') as f: + for p in range(0, parts): + part_dir = os.path.join( os.path.abspath(working_directory), 'task_%s' % p) + if not os.path.exists( part_dir ): + os.mkdir( part_dir ) + part_path = os.path.join(part_dir, os.path.basename(input_file)) + with open(part_path, 'w') as part_file: + for l in range(0, len_each): + part_file.write(f.readline()) + if remainder > 0: + part_file.write(f.readline()) + remainder -= 1 + outputs.append(part_path) + return outputs + +def split( input_file, working_directory, parts, file_type = None): + #Implement a better method for determining how to split. + if file_type.startswith('fastq'): + return split_fq(input_file, working_directory, parts) + else: + return split_txt(input_file, working_directory, parts) + +def merge( working_directory, output_file ): + output_file_name = os.path.basename(output_file) + task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith('task_')] + task_dirs.sort(key = lambda x: int(x.split('task_')[-1])) + for task_dir in task_dirs: + try: + os.system( 'cat %s >> %s' % ( os.path.join(task_dir, output_file_name), output_file ) ) + except Exception, e: + log.error(str(e))

1 0

galaxy-dist commit b1813ff5bb4e: Bug fixes and more UI streamlining for 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 Greg Von Kuster <greg(a)bx.psu.edu> # Date 1289426620 18000 # Node ID b1813ff5bb4ef20d0b5d5a1fdcfc16cf6ec3ba53 # Parent 0e5144e49c14eb2a77e1d3182a33b4f9c8de98fc Bug fixes and more UI streamlining for sample tracking. --- a/templates/requests/common/sample_datasets.mako +++ /dev/null @@ -1,5 +0,0 @@ -<%def name="render_sample_datasets( sample )"> - ${len( sample.datasets )} / ${len( sample.transferred_dataset_files )} -</%def> - -${render_sample_datasets( sample )} --- /dev/null +++ b/templates/requests/common/view_sample_datasets.mako @@ -0,0 +1,43 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/requests/common/common.mako" import="render_sample_datasets" /> + +<% + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + is_complete = sample.request.is_complete + is_submitted = sample.request.is_submitted + can_select_datasets = is_admin and ( is_complete or is_submitted ) + can_transfer_datasets = is_admin and sample.untransferred_dataset_files +%> + +<br/><br/> + +<ul class="manage-table-actions"> + %if can_transfer_datasets: + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Transfer datasets</a></li> + %endif + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ), transfer_status=transfer_status )}">Refresh page</a></li> + <li><a class="action-button" id="sample-${sample.id}-popup" class="menubutton">Dataset Actions</a></li> + <div popupmenu="sample-${sample.id}-popup"> + %if can_select_datasets: + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', cntrller=cntrller, request_id=trans.security.encode_id( sample.request.id ), sample_id=trans.security.encode_id( sample.id ) )}">Select more datasets</a></li> + %endif + <li><a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">View target Data Library</a></li> + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li> + </div> +</ul> + +%if message: + ${render_msg( message, status )} +%endif + +%if sample and sample_datasets: + ## The list of sample_datasets may not be the same as sample.datasets because it may be + ## filtered by a transfer_status value. The value of title changes based on this filter. + ${render_sample_datasets( cntrller, sample, sample_datasets, title )} +%else: + %if transfer_status: + No datasets with status ${transfer_status}" belong to this sample + %else: + No datasets have been selected for this sample. +%endif --- a/templates/requests/common/edit_samples.mako +++ b/templates/requests/common/edit_samples.mako @@ -41,15 +41,15 @@ %if can_submit: <li><a class="action-button" confirm="More samples cannot be added to this request after it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit request</a></li> %endif - <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request actions</a></li> + <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request Actions</a></li><div popupmenu="request-${request.id}-popup"><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> %if can_edit_request: - <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit this request</a> %endif <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> %if can_reject: - <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> %endif </div></ul> @@ -118,7 +118,7 @@ ## Render the other grids <% trans.sa_session.refresh( request.type.sample_form ) %> %for grid_index, grid_name in enumerate( request.type.sample_form.layout ): - ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), editing_samples=editing_samples )} + ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), current_samples=current_samples, editing_samples=editing_samples )} %endfor %else: <label>There are no samples.</label> --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1831,12 +1831,12 @@ class Sample( object ): return self.events[0] return None @property - def untransferred_dataset_files( self ): - untransferred_datasets = [] + def adding_to_library_dataset_files( self ): + adding_to_library_datasets = [] for dataset in self.datasets: - if dataset.status == SampleDataset.transfer_status.NOT_STARTED: - untransferred_datasets.append( dataset ) - return untransferred_datasets + if dataset.status == SampleDataset.transfer_status.ADD_TO_LIBRARY: + adding_to_library_datasets.append( dataset ) + return adding_to_library_datasets @property def inprogress_dataset_files( self ): inprogress_datasets = [] @@ -1845,12 +1845,40 @@ class Sample( object ): inprogress_datasets.append( dataset ) return inprogress_datasets @property + def queued_dataset_files( self ): + queued_datasets = [] + for dataset in self.datasets: + if dataset.status == SampleDataset.transfer_status.IN_QUEUE: + queued_datasets.append( dataset ) + return queued_datasets + @property + def transfer_error_dataset_files( self ): + transfer_error_datasets = [] + for dataset in self.datasets: + if dataset.status == SampleDataset.transfer_status.ERROR: + transfer_error_datasets.append( dataset ) + return transfer_error_datasets + @property def transferred_dataset_files( self ): transferred_datasets = [] for dataset in self.datasets: if dataset.status == SampleDataset.transfer_status.COMPLETE: transferred_datasets.append( dataset ) return transferred_datasets + @property + def transferring_dataset_files( self ): + transferring_datasets = [] + for dataset in self.datasets: + if dataset.status == SampleDataset.transfer_status.TRANSFERRING: + transferring_datasets.append( dataset ) + return transferring_datasets + @property + def untransferred_dataset_files( self ): + untransferred_datasets = [] + for dataset in self.datasets: + if dataset.status != SampleDataset.transfer_status.COMPLETE: + untransferred_datasets.append( dataset ) + return untransferred_datasets def get_untransferred_dataset_size( self, filepath ): # TODO: RC: If rsh keys are not set, this method will return something like the following: # greg(a)scofield.bx.psu.edu's password: 46M /afs/bx.psu.edu/home/greg/chr22/chr21.fa --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -109,10 +109,7 @@ class RequestsCommon( BaseController, Us "datasets": len( sample.datasets ), "html_state": unicode( trans.fill_template( "requests/common/sample_state.mako", sample=sample), - 'utf-8' ), - "html_datasets": unicode( trans.fill_template( "requests/common/sample_datasets.mako", - sample=sample ), - 'utf-8' ) } + 'utf-8' ) } return rval @web.expose @web.require_login( "create sequencing requests" ) @@ -455,7 +452,7 @@ class RequestsCommon( BaseController, Us samples.append( sample ) else: samples.append( None ) - # The __save_samples method requires samples widgets, not sample objects + # The __save_samples method requires sample_widgets, not sample objects samples = self.__get_sample_widgets( trans, request, samples, **kwd ) else: samples = current_samples @@ -699,9 +696,9 @@ class RequestsCommon( BaseController, Us # are in this state. retval = request.send_email_notification( trans, common_state, final_state ) if retval: - message = comments + retval + message = comment + retval else: - message = comments + message = comment if cntrller == 'api': return 200, message return trans.response.send_redirect( web.url_for( controller='requests_common', @@ -897,7 +894,7 @@ class RequestsCommon( BaseController, Us message=message ) ) @web.expose @web.require_login( "view data transfer page" ) - def view_selected_datasets( self, trans, cntrller, **kwd ): + def view_sample_datasets( self, trans, cntrller, **kwd ): # The link on the number of selected datasets will only appear if there is at least 1 selected dataset. # If there are 0 selected datasets, there is no link, so this method will only be reached from the requests # controller if there are selected datasets. @@ -930,13 +927,34 @@ class RequestsCommon( BaseController, Us if folder_path and folder_path[-1] != os.sep: folder_path += os.sep if not sample.request.type.datatx_info['host'] \ - or not sample.request.type.datatx_info['username'] \ - or not sample.request.type.datatx_info['password']: + or not sample.request.type.datatx_info[ 'username' ] \ + or not sample.request.type.datatx_info[ 'password' ]: status = 'error' message = 'The sequencer login information is incomplete. Click sequencer information to add login details.' - return trans.fill_template( '/requests/common/view_selected_datasets.mako', + transfer_status = params.get( 'transfer_status', None ) + if transfer_status in [ None, 'None' ]: + title = 'All selected datasets for "%s"' % sample.name + sample_datasets = sample.datasets + elif transfer_status == trans.model.SampleDataset.transfer_status.IN_QUEUE: + title = 'Datasets of "%s" that are in the transfer queue' % sample.name + sample_datasets = sample.queued_dataset_files + elif transfer_status == trans.model.SampleDataset.transfer_status.TRANSFERRING: + title = 'Datasets of "%s" that are being transferred' % sample.name + sample_datasets = sample.transferring_dataset_files + elif transfer_status == trans.model.SampleDataset.transfer_status.ADD_TO_LIBRARY: + title = 'Datasets of "%s" that are being added to the target data library' % sample.name + sample_datasets = sample.adding_to_library_dataset_files + elif transfer_status == trans.model.SampleDataset.transfer_status.COMPLETE: + title = 'Datasets of "%s" that are available in the target data library' % sample.name + sample_datasets = sample.transferred_dataset_files + elif transfer_status == trans.model.SampleDataset.transfer_status.ERROR: + title = 'Datasets of "%s" that resulted in a transfer error' % sample.name + sample_datasets = sample.transfer_error_dataset_files + return trans.fill_template( '/requests/common/view_sample_datasets.mako', cntrller=cntrller, sample=sample, + sample_datasets=sample_datasets, + transfer_status=transferr_status, message=message, status=status, files=[], @@ -1129,60 +1147,48 @@ class RequestsCommon( BaseController, Us # on a set of samples. library_id = params.get( 'sample_0_library_id', 'none' ) folder_id = params.get( 'sample_0_folder_id', 'none' ) - for index, obj in enumerate( sample_widgets ): - if obj is not None: - # obj will be None if the user checked sample check boxes and selected an action + for index, sample_widget in enumerate( sample_widgets ): + if sample_widget is not None: + # sample_widget will be None if the user checked sample check boxes and selected an action # to perform on multiple samples, but did not select certain samples. sample = request.samples[ index ] - # See if any values in kwd are different from the values already associated with this sample. - id_index = index + 1 - if sample_operation == 'none': - # We are handling changes to a single sample. - library_id = params.get( 'sample_%i_library_id' % id_index, 'none' ) - folder_id = params.get( 'sample_%i_folder_id' % id_index, 'none' ) - # Update the corresponding sample's values as well as the sample_widget. - name = util.restore_text( params.get( 'sample_%i_name' % index, '' ) ) - # The bar_code field requires special handling because after a request is submitted, the - # state of a sample cannot be changed without a bar_code associated with the sample. Bar - # codes can only be added to a sample after the request is submitted. Also, a samples will - # not have an associated SampleState until the request is submitted, at which time the sample - # is automatically associated with the first SamplesState configured by the admin for the - # request's RequestType. - bar_code = util.restore_text( params.get( 'sample_%i_barcode' % index, '' ) ) - if bar_code: - bc_message = self.__validate_barcode( trans, sample, bar_code ) - if bc_message: - kwd[ 'message' ] = bc_message - del kwd[ 'save_samples_button' ] - handle_error( **kwd ) - if not sample.bar_code: - # If the sample's associated SampleState is still the initial state - # configured by the admin for the request's RequestType, this must be - # the first time a bar code was added to the sample, so change it's state - # to the next associated SampleState. - if sample.state.id == request.type.states[0].id: - event = trans.app.model.SampleEvent(sample, - request.type.states[1], - 'Bar code associated with the sample' ) - trans.sa_session.add( event ) - trans.sa_session.flush() - library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) - field_values = [] - for field_index in range( len( request.type.sample_form.fields ) ): - field_values.append( util.restore_text( params.get( 'sample_%i_field_%i' % ( index, field_index ), '' ) ) ) + # Get the sample's form values to see if they have changed. form_values = trans.sa_session.query( trans.model.FormValues ).get( sample.values.id ) - form_values.content = field_values - if sample.name != name or \ - sample.bar_code != bar_code or \ - sample.library != library or \ - sample.folder != folder or \ - form_values.content != field_values: + if sample.name != sample_widget[ 'name' ] or \ + sample.bar_code != sample_widget[ 'barcode' ] or \ + sample.library != sample_widget[ 'library' ] or \ + sample.folder != sample_widget[ 'folder' ] or \ + form_values.content != sample_widget[ 'field_values' ]: # Information about this sample has been changed. - sample.name = name - sample.bar_code = bar_code - sample.library = library - sample.folder = folder - form_values.content = field_values + sample.name = sample_widget[ 'name' ] + barcode = sample_widget[ 'barcode' ] + # The bar_code field requires special handling because after a request is submitted, the + # state of a sample cannot be changed without a bar_code associated with the sample. Bar + # codes can only be added to a sample after the request is submitted. Also, a samples will + # not have an associated SampleState until the request is submitted, at which time the sample + # is automatically associated with the first SamplesState configured by the admin for the + # request's RequestType. + if barcode: + bc_message = self.__validate_barcode( trans, sample, bar_code ) + if bc_message: + kwd[ 'message' ] = bc_message + del kwd[ 'save_samples_button' ] + handle_error( **kwd ) + if not sample.bar_code: + # If the sample's associated SampleState is still the initial state + # configured by the admin for the request's RequestType, this must be + # the first time a bar code was added to the sample, so change it's state + # to the next associated SampleState. + if sample.state.id == request.type.states[0].id: + event = trans.app.model.SampleEvent(sample, + request.type.states[1], + 'Bar code associated with the sample' ) + trans.sa_session.add( event ) + trans.sa_session.flush() + sample.bar_code = barcode + sample.library = sample_widget[ 'library' ] + sample.folder = sample_widget[ 'folder' ] + form_values.content = sample_widget[ 'field_values' ] trans.sa_session.add_all( ( sample, form_values ) ) trans.sa_session.flush() def __get_library_and_folder( self, trans, library_id, folder_id ): @@ -1232,8 +1238,8 @@ class RequestsCommon( BaseController, Us """ Returns a list of dictionaries, each representing the widgets that define a sample on a form. The widgets are populated from kwd based on the set of samples received. The set of samples - corresponds to a reques.samples list, but if the user checked specific check boxes on the form, - those samples that were not check will have None objects in the list of samples. In this case, + corresponds to a request.samples list, but if the user checked specific check boxes on the form, + those samples that were not checked will have None objects in the list of samples. In this case, the corresponding sample_widget is populated from the db rather than kwd. """ params = util.Params( kwd ) @@ -1264,7 +1270,7 @@ class RequestsCommon( BaseController, Us bar_code = sample.bar_code library = sample.library folder = sample.folder - field_values = sample.values.content, + field_values = sample.values.content else: # Update the sample attributes from kwd name = util.restore_text( params.get( 'sample_%i_name' % index, sample.name ) ) @@ -1278,7 +1284,8 @@ class RequestsCommon( BaseController, Us library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) field_values = [] for field_index in range( len( request.type.sample_form.fields ) ): - field_values.append( util.restore_text( params.get( 'sample_%i_field_%i' % ( index, field_index ), '' ) ) ) + field_value = util.restore_text( params.get( 'sample_%i_field_%i' % ( index, field_index ), sample.values.content[ field_index ] ) ) + field_values.append( field_value ) library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans=trans, user=request.user, sample_index=id_index, --- a/templates/requests/common/find_samples.mako +++ b/templates/requests/common/find_samples.mako @@ -71,7 +71,7 @@ %else: State: ${sample.state.name}<br/> %endif - Datasets: <a href="${h.url_for( controller='requests_common', action='view_selected_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.transferred_dataset_files )}/${len( sample.datasets )}</a><br/> + Datasets: <a href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a><br/> %if is_admin: <i>User: ${sample.request.user.email}</i> %endif --- a/templates/requests/common/view_selected_datasets.mako +++ /dev/null @@ -1,37 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/requests/common/common.mako" import="render_sample_datasets" /> - -<% - is_admin = cntrller == 'requests_admin' and trans.user_is_admin() - is_complete = sample.request.is_complete - is_submitted = sample.request.is_submitted - can_select_datasets = is_admin and ( is_complete or is_submitted ) - can_transfer_datasets = is_admin and sample.untransferred_dataset_files -%> - -<br/><br/> - -<ul class="manage-table-actions"> - %if can_transfer_datasets: - <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Transfer datasets</a></li> - %endif - <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_selected_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Refresh page</a></li> - <li><a class="action-button" id="sample-${sample.id}-popup" class="menubutton">Dataset Actions</a></li> - <div popupmenu="sample-${sample.id}-popup"> - %if can_select_datasets: - <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', cntrller=cntrller, request_id=trans.security.encode_id( sample.request.id ), sample_id=trans.security.encode_id( sample.id ) )}">Select more datasets</a></li> - %endif - <li><a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">View target Data Library</a></li> - <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li> - </div> -</ul> - -%if message: - ${render_msg( message, status )} -%endif - -%if sample and sample.datasets: - <% title = 'Datasets currently selected for "sample.name"' %> - ${render_sample_datasets( cntrller, sample, sample.datasets, title )} -%endif --- a/templates/admin/requests/select_datasets_to_transfer.mako +++ b/templates/admin/requests/select_datasets_to_transfer.mako @@ -127,7 +127,7 @@ </div> %if sample and sample.datasets: - <% title = 'Datasets currently selected for "sample.name"' %> + <% title = 'Datasets currently selected for "%s"' % sample.name %><p/> ${render_sample_datasets( 'requests_admin', sample, sample.datasets, title )} %endif --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -100,8 +100,6 @@ // Replace HTML var cell1 = $("#sampleState-" + id); cell1.html( val.html_state ); - var cell2 = $("#sampleDatasets-" + id); - cell2.html( val.html_datasets ); sample_states[ parseInt( id ) ] = val.state; }); updater( sample_states ); @@ -115,14 +113,16 @@ </script></%def> -<%def name="render_editable_sample_row( is_admin, sample, current_sample_index, current_sample, encoded_selected_sample_ids )"> +<%def name="render_editable_sample_row( cntrller, sample, current_sample_index, current_sample, encoded_selected_sample_ids )"><% + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() if sample: trans.sa_session.refresh( sample.request ) is_complete = sample.request.is_complete is_rejected = request.is_rejected is_submitted = sample.request.is_submitted is_unsubmitted = sample.request.is_unsubmitted + can_delete_samples = not is_complete display_checkboxes = editing_samples and ( is_complete or is_rejected or is_submitted ) display_bar_code = request.samples and ( is_complete or is_rejected or is_submitted ) display_datasets = request.samples and ( is_complete or is_rejected or is_submitted ) @@ -130,6 +130,7 @@ is_complete = False is_submitted = False is_unsubmitted = False + can_delete_samples = False display_checkboxes = False display_bar_code = False display_datasets = False @@ -177,20 +178,36 @@ <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a> %elif sample.datasets: ## Only display a link if there is at least 1 selected dataset for the sample - <a href="${h.url_for( controller='requests_common', action='view_selected_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a></td> + <a href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a></td> %else: ${len( sample.datasets )} %endif </td><td valign="top"> - %if is_admin and sample.untransferred_dataset_files: - <a href="${h.url_for( controller='requests_common', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.transferred_dataset_files )}</a> + %if is_admin: + %if sample.untransferred_dataset_files: + ## At least 1 selected dataset is not yet transferred, so this link + ## will direct the admin to a page allowing them to transfer datasets. + <a href="${h.url_for( controller='requests_common', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.transferred_dataset_files )}</a> + %else: + ## All selected datasets have successfully transferred, so this link + ## will direct the admin to a page displaying all transferred datasets. + <a href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ), transfer_status=trans.model.SampleDataset.transfer_status.COMPLETE )}">${len( sample.transferred_dataset_files )}</a> + %endif %else: - ${len( sample.transferred_dataset_files )} + %if sample.transferred_dataset_files: + ## The cuurent user is not an admin, so this link will direct the + ## user to the target data library containing those datasets that + ## were successfully transferred. + <a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( sample.library.id ) )}">${len( sample.transferred_dataset_files )}</a> + %else: + ## Display a 0 with no link. + ${len( sample.transferred_dataset_files )} + %endif %endif </td> %endif - %if sample and ( is_admin or is_unsubmitted ) and not is_complete: + %if can_delete_samples: ## Delete button <td valign="top"><a class="action-button" href="${h.url_for( controller='requests_common', action='delete_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id=current_sample_index )}"><img src="${h.url_for('/static/images/delete_icon.png')}" style="cursor:pointer;"/></a></td> %endif @@ -206,7 +223,7 @@ is_submitted = request.is_submitted is_unsubmitted = request.is_unsubmitted can_add_samples = request.is_unsubmitted - can_delete_samples = request.samples and not is_complete + can_delete_samples = editing_samples and request.samples and not is_complete can_edit_samples = request.samples and ( is_admin or not is_complete ) can_select_datasets = is_admin and current_samples and ( is_submitted or is_complete ) display_checkboxes = editing_samples and ( is_complete or is_rejected or is_submitted ) @@ -271,7 +288,7 @@ sample = None %> %if editing_samples: - <tr>${render_editable_sample_row( is_admin, sample, current_sample_index, current_sample, encoded_selected_sample_ids )}</tr> + <tr>${render_editable_sample_row( cntrller, sample, current_sample_index, current_sample, encoded_selected_sample_ids )}</tr> %elif sample: <tr><td>${current_sample_name}</td> @@ -302,11 +319,11 @@ <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id= trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a> %else: ## If there are selected datasets, display them - <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_selected_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a> + <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a> %endif %elif sample.datasets: ## Only display a link if there is at least 1 selected dataset for the sample - <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_selected_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a> + <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a> %else: ${len( sample.datasets )} %endif @@ -322,7 +339,7 @@ </tr> %else: ## The Add sample button was clicked for this sample_widget - <tr>${render_editable_sample_row( is_admin, None, current_sample_index, current_sample, encoded_selected_sample_ids )}</tr> + <tr>${render_editable_sample_row( cntrller, None, current_sample_index, current_sample, encoded_selected_sample_ids )}</tr> %endif %endfor </tbody> @@ -390,7 +407,7 @@ </tr></%def> -<%def name="render_request_type_sample_form_grids( grid_index, grid_name, fields_dict, editing_samples )"> +<%def name="render_request_type_sample_form_grids( grid_index, grid_name, fields_dict, current_samples, editing_samples )"><% if not grid_name: grid_name = "Sample form layout " + grid_index @@ -432,6 +449,8 @@ </%def><%def name="render_sample_datasets( cntrller, sample, sample_datasets, title )"> + ## The list of sample_datasets may not be the same as sample.datasets because it may be + ## filtered by a transfer_status value. The value of title changes based on this filter. %if sample_datasets: <% is_admin = cntrller == 'requests_admin' and trans.user_is_admin() --- a/templates/requests/common/events.mako +++ b/templates/requests/common/events.mako @@ -4,6 +4,7 @@ <% is_admin = cntrller == 'requests_admin' and trans.user_is_admin() can_edit_request = ( is_admin and not request.is_complete ) or request.is_unsubmitted + can_reject_request = is_admin and request.is_submitted can_add_samples = request.is_unsubmitted %> @@ -13,14 +14,13 @@ <div popupmenu="request-${request.id}-popup"><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> %if can_edit_request: - <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit this request</a> %endif %if can_add_samples: - <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit</a> + <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit this request</a> %endif - %if is_admin and request.is_submitted: - <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> - <a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> + %if can_reject_request: + <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> %endif </div></ul> --- a/templates/requests/common/edit_basic_request_info.mako +++ b/templates/requests/common/edit_basic_request_info.mako @@ -12,11 +12,11 @@ <div popupmenu="request-${request.id}-popup"><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> %if can_add_samples: - <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit</a> + <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit this request</a> %endif <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> %if is_admin and request.is_submitted: - <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a><a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> %endif </div> --- a/templates/requests/common/view_request.mako +++ b/templates/requests/common/view_request.mako @@ -27,6 +27,7 @@ can_edit_samples = request.samples and ( is_admin or not is_complete ) can_reject = is_admin and is_submitted can_submit = request.samples and is_unsubmitted + can_undelete = request.deleted %><br/><br/> @@ -35,17 +36,17 @@ %if can_submit: <li><a class="action-button" confirm="More samples cannot be added to this request after it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit request</a></li> %endif - <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request actions</a></li> + <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request Actions</a></li><div popupmenu="request-${request.id}-popup"> - %if request.deleted: - <a class="action-button" href="${h.url_for( controller='requests_common', action='undelete_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Undelete</a> + %if can_undelete: + <a class="action-button" href="${h.url_for( controller='requests_common', action='undelete_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Undelete this request</a> %endif %if can_edit_request: - <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit this request</a> %endif <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> %if can_reject: - <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> %endif </div></ul> @@ -164,5 +165,5 @@ ## Render the other grids <% trans.sa_session.refresh( request.type.sample_form ) %> %for grid_index, grid_name in enumerate( request.type.sample_form.layout ): - ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), editing_samples=False )} + ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), current_samples=current_samples, editing_samples=False )} %endfor

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galaxy-dist commit bbc0f56e3e16: A few more bug fixes in the new sample tracking code.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1289427445 18000 # Node ID bbc0f56e3e16f93bf3c81d09b0fa12876a3f2579 # Parent b1813ff5bb4ef20d0b5d5a1fdcfc16cf6ec3ba53 A few more bug fixes in the new sample tracking code. --- a/templates/admin/requests/select_datasets_to_transfer.mako +++ b/templates/admin/requests/select_datasets_to_transfer.mako @@ -127,7 +127,7 @@ </div> %if sample and sample.datasets: - <% title = 'Datasets currently selected for "%s"' % sample.name %> + <% title = 'All selected datasets for "%s"' % sample.name %><p/> ${render_sample_datasets( 'requests_admin', sample, sample.datasets, title )} %endif --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -952,9 +952,10 @@ class RequestsCommon( BaseController, Us sample_datasets = sample.transfer_error_dataset_files return trans.fill_template( '/requests/common/view_sample_datasets.mako', cntrller=cntrller, + title=title, sample=sample, sample_datasets=sample_datasets, - transfer_status=transferr_status, + transfer_status=transfer_status, message=message, status=status, files=[], --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -329,10 +329,26 @@ %endif </td><td> - %if is_admin and sample.untransferred_dataset_files: - <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.transferred_dataset_files )}</a> + %if is_admin: + %if sample.untransferred_dataset_files: + ## At least 1 selected dataset is not yet transferred, so this link + ## will direct the admin to a page allowing them to transfer datasets. + <a href="${h.url_for( controller='requests_common', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.transferred_dataset_files )}</a> + %else: + ## All selected datasets have successfully transferred, so this link + ## will direct the admin to a page displaying all transferred datasets. + <a href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ), transfer_status=trans.model.SampleDataset.transfer_status.COMPLETE )}">${len( sample.transferred_dataset_files )}</a> + %endif %else: - ${len( sample.transferred_dataset_files )} + %if sample.transferred_dataset_files: + ## The cuurent user is not an admin, so this link will direct the + ## user to the target data library containing those datasets that + ## were successfully transferred. + <a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( sample.library.id ) )}">${len( sample.transferred_dataset_files )}</a> + %else: + ## Display a 0 with no link. + ${len( sample.transferred_dataset_files )} + %endif %endif </td> %endif --- a/templates/requests/common/view_sample_datasets.mako +++ b/templates/requests/common/view_sample_datasets.mako @@ -40,4 +40,5 @@ No datasets with status ${transfer_status}" belong to this sample %else: No datasets have been selected for this sample. + %endif %endif

1 0

galaxy-dist commit 865d7175847a: Corrected bug in reference to genome file in NGS simulation 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 Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1289492971 18000 # Node ID 865d7175847ad322959f6b85532357d0f69afa46 # Parent 591c53b44ae4a6237a841adaa3abfe59829beebe Corrected bug in reference to genome file in NGS simulation tool --- a/tools/ngs_simulation/ngs_simulation.xml +++ b/tools/ngs_simulation/ngs_simulation.xml @@ -5,7 +5,7 @@ ngs_simulation.py #if $in_type.input_type == "built-in" --input="${ filter( lambda x: str( x[0] ) == str( $in_type.genome ), $__app__.tool_data_tables[ 'ngs_sim_fasta' ].get_fields() )[0][-1] }" - --genome=$genome + --genome=$in_type.genome #else --input=$in_type.input1 #end if

1 0

galaxy-dist commit 7ea4c156ae32: Add a pop-up menu for a sample if it is possible to either select datasets to transfer or transfer selected datasets for the sample. Also use better naming convention for a key variable name.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1289492968 18000 # Node ID 7ea4c156ae32c4757378229bfc49584df91a024a # Parent 591c53b44ae4a6237a841adaa3abfe59829beebe Add a pop-up menu for a sample if it is possible to either select datasets to transfer or transfer selected datasets for the sample. Also use better naming convention for a key variable name. --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -212,14 +212,14 @@ class RequestsCommon( BaseController, Us except: return invalid_id_redirect( trans, cntrller, request_id ) sample_state_id = params.get( 'sample_state_id', None ) - # Get the user entered sample information - current_samples = self.__get_sample_widgets( trans, request, request.samples, **kwd ) + # Build a list of sample widgets (based on the attributes of each sample) for display. + displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd ) request_widgets = self.__get_request_widgets( trans, request.id ) return trans.fill_template( '/requests/common/view_request.mako', cntrller=cntrller, request=request, request_widgets=request_widgets, - current_samples=current_samples, + displayable_sample_widgets=displayable_sample_widgets, status=status, message=message ) @web.expose @@ -415,8 +415,8 @@ class RequestsCommon( BaseController, Us editing_samples=editing_samples ) ) # Get all libraries for which the current user has permission to add items. libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) - # Get the user entered sample information - current_samples = self.__get_sample_widgets( trans, request, request.samples, **kwd ) + # Build a list of sample widgets (based on the attributes of each sample) for display. + displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd ) encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) sample_operation = params.get( 'sample_operation', 'none' ) def handle_error( **kwd ): @@ -433,14 +433,17 @@ class RequestsCommon( BaseController, Us handle_error( **kwd ) if params.get( 'import_samples_button', False ): # Import sample field values from a csv file - return self.__import_samples( trans, cntrller, request, current_samples, libraries, **kwd ) + return self.__import_samples( trans, cntrller, request, displayable_sample_widgets, libraries, **kwd ) elif params.get( 'add_sample_button', False ): return self.add_sample( trans, cntrller, request_id, **kwd ) elif params.get( 'save_samples_button', False ): if encoded_selected_sample_ids: - # This gets tricky because we need the list of samples to include the same number - # of objects that that current_samples ( i.e., request.samples ) has. We'll first - # get the set of samples corresponding to the checked sample ids. + # We need the list of displayable_sample_widgets to include the same number + # of objects that that request.samples has so that we can enumerate over each + # list without problems. We have to be careful here since the user may have + # used the multi-select check boxes when editing sample widgets, but didn't + # select all of them. We'll first get the set of samples corresponding to the + # checked sample ids. samples = [] selected_samples = [] for encoded_sample_id in encoded_selected_sample_ids: @@ -453,12 +456,12 @@ class RequestsCommon( BaseController, Us else: samples.append( None ) # The __save_samples method requires sample_widgets, not sample objects - samples = self.__get_sample_widgets( trans, request, samples, **kwd ) + sample_widgets = self.__get_sample_widgets( trans, request, samples, **kwd ) else: - samples = current_samples - return self.__save_samples( trans, cntrller, request, samples, **kwd ) + sample_widgets = displayable_sample_widgets + return self.__save_samples( trans, cntrller, request, sample_widgets, **kwd ) request_widgets = self.__get_request_widgets( trans, request.id ) - sample_copy = self.__build_copy_sample_select_field( trans, current_samples ) + sample_copy = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) libraries_select_field, folders_select_field = self.__build_library_and_folder_select_fields( trans, request.user, 0, @@ -473,7 +476,7 @@ class RequestsCommon( BaseController, Us request=request, encoded_selected_sample_ids=encoded_selected_sample_ids, request_widgets=request_widgets, - current_samples=current_samples, + displayable_sample_widgets=displayable_sample_widgets, sample_copy=sample_copy, libraries=libraries, sample_operation_select_field=sample_operation_select_field, @@ -805,12 +808,12 @@ class RequestsCommon( BaseController, Us is_admin = cntrller == 'requests_admin' and trans.user_is_admin() # Get the widgets for rendering the request form request_widgets = self.__get_request_widgets( trans, request.id ) - current_samples = self.__get_sample_widgets( trans, request, request.samples, **kwd ) - if not current_samples: + displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd ) + if not displayable_sample_widgets: # Form field names are zero-based. sample_index = 0 else: - sample_index = len( current_samples ) + sample_index = len( displayable_sample_widgets ) if params.get( 'add_sample_button', False ): # Get all libraries for which the current user has permission to add items libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) @@ -818,18 +821,18 @@ class RequestsCommon( BaseController, Us # See if the user has selected a sample to copy. copy_sample_index = int( params.get( 'copy_sample_index', -1 ) ) for index in range( num_samples_to_add ): - id_index = len( current_samples ) + 1 + id_index = len( displayable_sample_widgets ) + 1 if copy_sample_index != -1: # 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' % ( len( current_samples ) + 1 ) - field_values = [ val for val in current_samples[ copy_sample_index ][ 'field_values' ] ] + library_id = displayable_sample_widgets[ copy_sample_index][ 'library_select_field' ].get_selected( return_value=True ) + folder_id = displayable_sample_widgets[ copy_sample_index ][ 'folder_select_field' ].get_selected( return_value=True ) + name = displayable_sample_widgets[ copy_sample_index ][ 'name' ] + '_%i' % ( len( displayable_sample_widgets ) + 1 ) + field_values = [ val for val in displayable_sample_widgets[ copy_sample_index ][ 'field_values' ] ] else: # The user has not selected a sample to copy, just adding a new generic sample. library_id = None folder_id = None - name = 'Sample_%i' % ( len( current_samples ) + 1 ) + name = 'Sample_%i' % ( len( displayable_sample_widgets ) + 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, @@ -841,25 +844,26 @@ class RequestsCommon( BaseController, Us folder_id=folder_id, **kwd ) # Append the new sample to the current list of samples for the request - current_samples.append( dict( name=name, - barcode='', - library=None, - library_id=library_id, - folder=None, - folder_id=folder_id, - field_values=field_values, - library_select_field=library_select_field, - folder_select_field=folder_select_field ) ) + displayable_sample_widgets.append( dict( id=None, + name=name, + barcode='', + library=None, + library_id=library_id, + folder=None, + folder_id=folder_id, + field_values=field_values, + library_select_field=library_select_field, + folder_select_field=folder_select_field ) ) encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) sample_operation = params.get( 'sample_operation', 'none' ) sample_operation_select_field = self.__build_sample_operation_select_field( trans, is_admin, request, sample_operation ) - sample_copy = self.__build_copy_sample_select_field( trans, current_samples ) + sample_copy = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) return trans.fill_template( '/requests/common/edit_samples.mako', cntrller=cntrller, request=request, encoded_selected_sample_ids=encoded_selected_sample_ids, request_widgets=request_widgets, - current_samples=current_samples, + displayable_sample_widgets=displayable_sample_widgets, sample_operation_select_field=sample_operation_select_field, sample_copy=sample_copy, editing_samples=False, @@ -876,9 +880,9 @@ class RequestsCommon( BaseController, Us request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) except: return invalid_id_redirect( trans, cntrller, request_id ) - current_samples = self.__get_sample_widgets( trans, request, request.samples, **kwd ) + displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd ) sample_index = int( params.get( 'sample_id', 0 ) ) - sample_name = current_samples[sample_index]['name'] + sample_name = displayable_sample_widgets[sample_index]['name'] sample = request.has_sample( sample_name ) if sample: trans.sa_session.delete( sample.values ) @@ -960,7 +964,7 @@ class RequestsCommon( BaseController, Us status=status, files=[], folder_path=folder_path ) - def __import_samples( self, trans, cntrller, request, current_samples, libraries, **kwd ): + def __import_samples( self, trans, cntrller, request, displayable_sample_widgets, libraries, **kwd ): """ Reads the samples csv file and imports all the samples. The format of the csv file is: SampleName,DataLibrary,DataLibraryFolder,Field1,Field2.... @@ -987,19 +991,20 @@ class RequestsCommon( BaseController, Us folder_id = folder.id library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans, request.user, - len( current_samples ), + len( displayable_sample_widgets ), libraries, None, library_id, folder_id, **kwd ) - current_samples.append( dict( name=row[0], - barcode='', - library=None, - folder=None, - library_select_field=library_select_field, - folder_select_field=folder_select_field, - field_values=row[3:] ) ) + displayable_sample_widgets.append( dict( id=None, + name=row[0], + barcode='', + library=None, + folder=None, + library_select_field=library_select_field, + folder_select_field=folder_select_field, + field_values=row[3:] ) ) except Exception, e: if str( e ) == "'unicode' object has no attribute 'file'": message = "Select a file" @@ -1014,12 +1019,12 @@ class RequestsCommon( BaseController, Us status='error', message=message ) ) request_widgets = self.__get_request_widgets( trans, request.id ) - sample_copy = self.__build_copy_sample_select_field( trans, current_samples ) + sample_copy = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) return trans.fill_template( '/requests/common/edit_samples.mako', cntrller=cntrller, request=request, request_widgets=request_widgets, - current_samples=current_samples, + displayable_sample_widgets=displayable_sample_widgets, sample_copy=sample_copy, editing_samples=False ) def __save_samples( self, trans, cntrller, request, samples, **kwd ): @@ -1110,17 +1115,17 @@ class RequestsCommon( BaseController, Us # by the admin ( i.e., the sample's SampleState would be set to request.type.states[0] ). for index in range( len( samples ) - len( request.samples ) ): sample_index = len( request.samples ) - current_sample = samples[ sample_index ] - form_values = trans.model.FormValues( request.type.sample_form, current_sample[ 'field_values' ] ) + sample_widget = samples[ sample_index ] + form_values = trans.model.FormValues( request.type.sample_form, sample_widget[ 'field_values' ] ) trans.sa_session.add( form_values ) trans.sa_session.flush() - s = trans.model.Sample( name=current_sample[ 'name' ], + s = trans.model.Sample( name=sample_widget[ 'name' ], desc='', request=request, form_values=form_values, bar_code='', - library=current_sample[ 'library' ], - folder=current_sample[ 'folder' ] ) + library=sample_widget[ 'library' ], + folder=sample_widget[ 'folder' ] ) trans.sa_session.add( s ) trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests_common', @@ -1264,9 +1269,9 @@ class RequestsCommon( BaseController, Us for index, sample in enumerate( samples ): id_index = index + 1 if sample is None: - # Id sample is None, then we'll use the sample from the request object since it will - # not have updated =values from kwd. + # Use the sample from the request object since it will not have updated values from kwd. sample = request.samples[ index ] + sample_id = sample.id name = sample.name bar_code = sample.bar_code library = sample.library @@ -1274,6 +1279,7 @@ class RequestsCommon( BaseController, Us field_values = sample.values.content else: # Update the sample attributes from kwd + sample_id = None name = util.restore_text( params.get( 'sample_%i_name' % index, sample.name ) ) bar_code = util.restore_text( params.get( 'sample_%i_barcode' % index, sample.bar_code ) ) library_id = util.restore_text( params.get( 'sample_%i_library_id' % id_index, '' ) ) @@ -1295,7 +1301,8 @@ class RequestsCommon( BaseController, Us library_id=library_id, folder_id=folder_id, **kwd ) - sample_widgets.append( dict( name=name, + sample_widgets.append( dict( id=sample_id, + name=name, barcode=bar_code, library=library, folder=folder, @@ -1325,7 +1332,8 @@ class RequestsCommon( BaseController, Us library_id=library_id, folder_id=folder_id, **kwd ) - sample_widgets.append( dict( name=name, + sample_widgets.append( dict( id=None, + name=name, barcode=bar_code, library=library, folder=folder, @@ -1335,10 +1343,10 @@ class RequestsCommon( BaseController, Us index += 1 return sample_widgets # ===== Methods for building SelectFields used on various request forms ===== - def __build_copy_sample_select_field( self, trans, current_samples ): + def __build_copy_sample_select_field( self, trans, displayable_sample_widgets ): copy_sample_index_select_field = SelectField( 'copy_sample_index' ) copy_sample_index_select_field.add_option( 'None', -1, selected=True ) - for index, sample_dict in enumerate( current_samples ): + for index, sample_dict in enumerate( displayable_sample_widgets ): copy_sample_index_select_field.add_option( sample_dict[ 'name' ], index ) return copy_sample_index_select_field def __build_request_type_id_select_field( self, trans, selected_value='none' ): @@ -1458,20 +1466,20 @@ class RequestsCommon( BaseController, Us message += '<b>' + ef + '</b> ' return message return None - def __validate_sample_names( self, trans, cntrller, request, current_samples, **kwd ): + def __validate_sample_names( self, trans, cntrller, request, displayable_sample_widgets, **kwd ): # Check for duplicate sample names for all samples of the request. editing_samples = util.string_as_bool( kwd.get( 'editing_samples', False ) ) message = '' - for index in range( len( current_samples ) - len( request.samples ) ): + for index in range( len( displayable_sample_widgets ) - len( request.samples ) ): sample_index = index + len( request.samples ) - current_sample = current_samples[ sample_index ] - sample_name = current_sample[ 'name' ] + sample_widget = displayable_sample_widgets[ sample_index ] + sample_name = sample_widget[ 'name' ] if not sample_name.strip(): message = 'Enter the name of sample number %i' % sample_index break count = 0 - for i in range( len( current_samples ) ): - if sample_name == current_samples[ i ][ 'name' ]: + for i in range( len( displayable_sample_widgets ) ): + if sample_name == displayable_sample_widgets[ i ][ 'name' ]: count += 1 if count > 1: message = "You tried to add %i samples with the name (%s). Samples belonging to a request must have unique names." % ( count, sample_name ) --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -113,7 +113,7 @@ </script></%def> -<%def name="render_editable_sample_row( cntrller, sample, current_sample_index, current_sample, encoded_selected_sample_ids )"> +<%def name="render_editable_sample_row( cntrller, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids )"><% is_admin = cntrller == 'requests_admin' and trans.user_is_admin() if sample: @@ -145,7 +145,7 @@ <td><input type="checkbox" name=select_sample_${sample.id} id="sample_checkbox" value="true" ${checked_str}/><input type="hidden" name=select_sample_${sample.id} id="sample_checkbox" value="true"/></td> %endif <td valign="top"> - <input type="text" name="sample_${current_sample_index}_name" value="${current_sample['name']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_name" value="${sample_widget['name']}" size="10"/><div class="toolParamHelp" style="clear: both;"><i>${' (required)' }</i></div> @@ -153,10 +153,10 @@ %if display_bar_code: <td valign="top"> %if is_admin: - <input type="text" name="sample_${current_sample_index}_barcode" value="${current_sample['barcode']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_barcode" value="${sample_widget['barcode']}" size="10"/> %else: - ${current_sample['barcode']} - <input type="hidden" name="sample_${current_sample_index}_barcode" value="${current_sample['barcode']}"/> + ${sample_widget['barcode']} + <input type="hidden" name="sample_${sample_widget_index}_barcode" value="${sample_widget['barcode']}"/> %endif </td> %endif @@ -169,8 +169,8 @@ %else: <td></td> %endif - <td valign="top">${current_sample['library_select_field'].get_html()}</td> - <td valign="top">${current_sample['folder_select_field'].get_html()}</td> + <td valign="top">${sample_widget['library_select_field'].get_html()}</td> + <td valign="top">${sample_widget['folder_select_field'].get_html()}</td> %if display_datasets: <td valign="top"> ## An admin can select the datasets to transfer, while a non-admin can only view what has been selected @@ -220,11 +220,11 @@ %endif %if can_delete_samples: ## Delete button - <td valign="top"><a class="action-button" href="${h.url_for( controller='requests_common', action='delete_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id=current_sample_index )}"><img src="${h.url_for('/static/images/delete_icon.png')}" style="cursor:pointer;"/></a></td> + <td valign="top"><a class="action-button" href="${h.url_for( controller='requests_common', action='delete_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id=sample_widget_index )}"><img src="${h.url_for('/static/images/delete_icon.png')}" style="cursor:pointer;"/></a></td> %endif </%def> -<%def name="render_samples_grid( cntrller, request, current_samples, action, editing_samples=False, encoded_selected_sample_ids=[], render_buttons=False, grid_header='<h3>Samples</h3>' )"> +<%def name="render_samples_grid( cntrller, request, displayable_sample_widgets, action, editing_samples=False, encoded_selected_sample_ids=[], render_buttons=False, grid_header='<h3>Samples</h3>' )"> ## Displays the "Samples" grid <% trans.sa_session.refresh( request ) @@ -236,7 +236,8 @@ can_add_samples = request.is_unsubmitted can_delete_samples = editing_samples and request.samples and not is_complete can_edit_samples = request.samples and ( is_admin or not is_complete ) - can_select_datasets = is_admin and current_samples and ( is_submitted or is_complete ) + can_select_datasets = is_admin and displayable_sample_widgets and ( is_submitted or is_complete ) + can_transfer_datasets = is_admin and request.samples and not request.is_rejected display_checkboxes = editing_samples and ( is_complete or is_rejected or is_submitted ) display_bar_code = request.samples and ( is_complete or is_rejected or is_submitted ) display_datasets = request.samples and ( is_complete or is_submitted ) @@ -278,46 +279,67 @@ <thead><tbody><% trans.sa_session.refresh( request ) %> - ## current_samples is a dictionary whose keys are: - ## name, barcode, library, folder, field_values, library_select_field, folder_select_field - %for current_sample_index, current_sample in enumerate( current_samples ): + ## displayable_sample_widgets is a dictionary whose keys are: + ## id, name, barcode, library, folder, field_values, library_select_field, folder_select_field + ## A displayable_sample_widget will have an id == None if the widget's associated sample has not + ## yet been saved (i.e., the use clicked the "Add sample" button but has not yet clicked the + ## "Save" button. + %for sample_widget_index, sample_widget in enumerate( displayable_sample_widgets ): <% - current_sample_name = current_sample[ 'name' ] - current_sample_barcode = current_sample[ 'barcode' ] - current_sample_library = current_sample[ 'library' ] - if current_sample_library: + sample_widget_name = sample_widget[ 'name' ] + sample_widget_barcode = sample_widget[ 'barcode' ] + sample_widget_library = sample_widget[ 'library' ] + if sample_widget_library: if cntrller == 'requests': library_cntrller = 'library' elif is_admin: library_cntrller = 'library_admin' else: library_cntrller = None - current_sample_folder = current_sample[ 'folder' ] + sample_widget_folder = sample_widget[ 'folder' ] try: - sample = request.samples[ current_sample_index ] + sample = request.samples[ sample_widget_index ] except: sample = None %> %if editing_samples: - <tr>${render_editable_sample_row( cntrller, sample, current_sample_index, current_sample, encoded_selected_sample_ids )}</tr> + <tr>${render_editable_sample_row( cntrller, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids )}</tr> %elif sample: <tr> - <td>${current_sample_name}</td> + <td> + %if sample.state and ( can_select_datasets or can_transfer_datasets ): + ## A sample will have a state only after the request has been submitted. + <% encoded_id = trans.security.encode_id( sample.id ) %> + <div style="float: left; margin-left: 2px;" class="menubutton split popup" id="sample-${sample.id}-popup"> + ${sample.name} + </div> + <div popupmenu="sample-${sample.id}-popup"> + %if can_select_datasets: + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ), sample_id=trans.security.encode_id( sample.id ) )}">Select datasets to transfer</a></li> + %endif + %if sample.untransferred_dataset_files: + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Transfer datasets</a></li> + %endif + </div> + %else: + ${sample_widget_name} + %endif + </td> %if display_bar_code: - <td>${current_sample_barcode}</td> + <td>${sample_widget_barcode}</td> %endif %if is_unsubmitted: <td>Unsubmitted</td> %else: <td><a id="sampleState-${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 current_sample_library and library_cntrller is not None: - <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( current_sample_library.id ) )}">${current_sample_library.name}</a></td> + %if sample_widget_library and library_cntrller is not None: + <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name}</a></td> %else: <td></td> %endif - %if current_sample_folder: - <td>${current_sample_folder.name}</td> + %if sample_widget_folder: + <td>${sample_widget_folder.name}</td> %else: <td></td> %endif @@ -371,7 +393,7 @@ </tr> %else: ## The Add sample button was clicked for this sample_widget - <tr>${render_editable_sample_row( cntrller, None, current_sample_index, current_sample, encoded_selected_sample_ids )}</tr> + <tr>${render_editable_sample_row( cntrller, None, sample_widget_index, sample_widget, encoded_selected_sample_ids )}</tr> %endif %endfor </tbody> @@ -439,7 +461,7 @@ </tr></%def> -<%def name="render_request_type_sample_form_grids( grid_index, grid_name, fields_dict, current_samples, editing_samples )"> +<%def name="render_request_type_sample_form_grids( grid_index, grid_name, fields_dict, displayable_sample_widgets, editing_samples )"><% if not grid_name: grid_name = "Sample form layout " + grid_index @@ -466,7 +488,7 @@ <thead><tbody><% trans.sa_session.refresh( request ) %> - %for sample_index, sample in enumerate( current_samples ): + %for sample_index, sample in enumerate( displayable_sample_widgets ): <% if editing_samples or sample_index >= len( request.samples ): display_only = False @@ -505,7 +527,7 @@ <tr><td> %if is_admin: - <% encoded_id = trans.security.encode_id(dataset.id) %> + <% encoded_id = trans.security.encode_id( dataset.id ) %><span class="expandLink dataset-${dataset}-click"><span class="rowIcon"></span><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="dataset-${dataset.id}-popup"><a class="dataset-${encoded_id}-click" href="${h.url_for( controller='requests_admin', action='manage_datasets', operation='view', id=trans.security.encode_id( dataset.id ) )}">${dataset.name}</a> --- a/templates/requests/common/edit_samples.mako +++ b/templates/requests/common/edit_samples.mako @@ -72,14 +72,14 @@ <div class="toolFormBody"><form id="edit_samples" name="edit_samples" action="${h.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ), editing_samples=editing_samples )}" method="post"> - %if current_samples: + %if displayable_sample_widgets: <% if editing_samples: grid_header = '<h3>Edit Current Samples of Request "%s"</h3>' % request.name else: grid_header = '<h3>Add Samples to Request "%s"</h3>' % request.name %> - ${render_samples_grid( cntrller, request, current_samples, action='edit_samples', editing_samples=editing_samples, encoded_selected_sample_ids=encoded_selected_sample_ids, render_buttons=False, grid_header=grid_header )} + ${render_samples_grid( cntrller, request, displayable_sample_widgets, action='edit_samples', editing_samples=editing_samples, encoded_selected_sample_ids=encoded_selected_sample_ids, render_buttons=False, grid_header=grid_header )} %if editing_samples and len( sample_operation_select_field.options ) > 1 and not is_unsubmitted: <div class="form-row" style="background-color:#FAFAFA;"> For selected samples: @@ -118,14 +118,14 @@ ## Render the other grids <% trans.sa_session.refresh( request.type.sample_form ) %> %for grid_index, grid_name in enumerate( request.type.sample_form.layout ): - ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), current_samples=current_samples, editing_samples=editing_samples )} + ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, editing_samples=editing_samples )} %endfor %else: <label>There are no samples.</label> %endif %if not editing_samples and is_unsubmitted: ## The user is adding a new sample - %if current_samples: + %if displayable_sample_widgets: <p/><div class="form-row"><label> Copy <input type="text" name="num_sample_to_copy" value="1" size="3"/> samples from sample ${sample_copy.get_html()}</label> @@ -138,7 +138,7 @@ <div class="form-row"> ## hidden element to make twill work. <input type="hidden" name="hidden_input" value=""/> - %if ( request.samples or current_samples ) and ( editing_samples or len( current_samples ) > len( request.samples ) ): + %if ( request.samples or displayable_sample_widgets ) and ( editing_samples or len( displayable_sample_widgets ) > len( request.samples ) ): <input type="submit" name="add_sample_button" value="Add sample" /><input type="submit" name="save_samples_button" value="Save"/><input type="submit" name="cancel_changes_button" value="Cancel"/> --- a/templates/requests/common/view_request.mako +++ b/templates/requests/common/view_request.mako @@ -148,12 +148,12 @@ </div></div><p/> -%if current_samples: +%if displayable_sample_widgets: <% grid_header = '<h3>Samples</h3>' render_buttons = can_edit_samples %> - ${render_samples_grid( cntrller, request, current_samples=current_samples, action='view_request', editing_samples=False, encoded_selected_sample_ids=[], render_buttons=render_buttons, grid_header=grid_header )} + ${render_samples_grid( cntrller, request, displayable_sample_widgets=displayable_sample_widgets, action='view_request', editing_samples=False, encoded_selected_sample_ids=[], render_buttons=render_buttons, grid_header=grid_header )} %else: There are no samples. %if can_add_samples: @@ -165,5 +165,5 @@ ## Render the other grids <% trans.sa_session.refresh( request.type.sample_form ) %> %for grid_index, grid_name in enumerate( request.type.sample_form.layout ): - ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), current_samples=current_samples, editing_samples=False )} + ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, editing_samples=False )} %endfor

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