June 2010 - galaxy-commits - lists.galaxyproject.org

galaxy-dist commit a76d05bb41e1: Fixes and enhancements to the reports webapp:
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '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 1275672554 14400 # Node ID a76d05bb41e1c1f1eeaa93a18289eeed1213199b # Parent dd69c382eff1d3c0c160bc3ec392b06671317fd0 Fixes and enhancements to the reports webapp: 0) The report that is initially displayed is now the number of jobs per day for the current month rather than the grid displaying all jobs for today. 1) Eliminate eagerloading when querying jobs so that queries are much faster 2) Fix the disk space ( system ) report, and add a new feature that displays all active ( undeleted ) hda and ldda pointers to a specific dataset. 3) Standardize request parameters so that queries can more easily be built using parameters from the request. 4) A few other miscellaneous bug fixes in the reports. --- a/templates/webapps/reports/registered_users.mako +++ b/templates/webapps/reports/registered_users.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> --- a/templates/webapps/reports/jobs_user_per_month.mako +++ b/templates/webapps/reports/jobs_user_per_month.mako @@ -4,7 +4,7 @@ <% from galaxy import util %> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> @@ -27,7 +27,7 @@ <tr class="tr"> %endif <td>${job[2]} ${job[3]}</td> - <td><a href="${h.url_for( controller='jobs', action='user_for_month', email=email, month=job[0] )}">${job[1]}</a></td> + <td><a href="${h.url_for( controller='jobs', action='user_for_month', email=email, specified_date=job[0]+'-01' )}">${job[1]}</a></td></tr><% ctr += 1 %> %endfor --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -63,7 +63,7 @@ class SpecifiedDateListGrid( grids.Grid model_class=model.User, link=( lambda item: dict( operation="user_per_month", id=item.id, webapp="reports" ) ), attach_popup=False ), - grids.StateColumn( "All", key="state", model_class=model.Job, visible=False, filterable="advanced" ) + grids.StateColumn( "state", key="state", model_class=model.Job, visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[1], columns[2] ], @@ -78,45 +78,59 @@ class SpecifiedDateListGrid( grids.Grid def build_initial_query( self, trans, **kwd ): specified_date = kwd.get( 'specified_date', 'All' ) if specified_date == 'All': - return trans.sa_session.query( self.model_class ) + return trans.sa_session.query( self.model_class ) \ + .enable_eagerloads( False ) year, month, day = map( int, specified_date.split( "-" ) ) start_date = date( year, month, day ) end_date = start_date + timedelta( days=1 ) - return trans.sa_session.query( self.model_class ).filter( and_( self.model_class.table.c.create_time >= start_date, - self.model_class.table.c.create_time < end_date ) ) + return trans.sa_session.query( self.model_class ) \ + .filter( and_( self.model_class.table.c.create_time >= start_date, + self.model_class.table.c.create_time < end_date ) ) \ + .enable_eagerloads( False ) class SpecifiedDateInErrorListGrid( SpecifiedDateListGrid ): def build_initial_query( self, trans, **kwd ): specified_date = kwd.get( 'specified_date', 'All' ) if specified_date == 'All': - return trans.sa_session.query( self.model_class ).filter( self.model_class.table.c.state == model.Job.states.ERROR ) + return trans.sa_session.query( self.model_class ) \ + .filter( self.model_class.table.c.state == model.Job.states.ERROR ) \ + .enable_eagerloads( False ) year, month, day = map( int, specified_date.split( "-" ) ) start_date = date( year, month, day ) end_date = start_date + timedelta( days=1 ) - return trans.sa_session.query( self.model_class ).filter( and_( self.model_class.table.c.state == model.Job.states.ERROR, - self.model_class.table.c.create_time >= start_date, - self.model_class.table.c.create_time < end_date ) ) + return trans.sa_session.query( self.model_class ) \ + .filter( and_( self.model_class.table.c.state == model.Job.states.ERROR, + self.model_class.table.c.create_time >= start_date, + self.model_class.table.c.create_time < end_date ) ) \ + .enable_eagerloads( False ) class AllUnfinishedListGrid( SpecifiedDateListGrid ): def build_initial_query( self, trans, **kwd ): specified_date = kwd.get( 'specified_date', 'All' ) if specified_date == 'All': - return trans.sa_session.query( self.model_class ).filter( not_( or_( model.Job.table.c.state == model.Job.states.OK, - model.Job.table.c.state == model.Job.states.ERROR, - model.Job.table.c.state == model.Job.states.DELETED ) ) ) + return trans.sa_session.query( self.model_class ) \ + .filter( not_( or_( model.Job.table.c.state == model.Job.states.OK, + model.Job.table.c.state == model.Job.states.ERROR, + model.Job.table.c.state == model.Job.states.DELETED ) ) ) \ + .enable_eagerloads( False ) year, month, day = map( int, specified_date.split( "-" ) ) start_date = date( year, month, day ) end_date = start_date + timedelta( days=1 ) - return trans.sa_session.query( self.model_class ).filter( and_( not_( or_( model.Job.table.c.state == model.Job.states.OK, - model.Job.table.c.state == model.Job.states.ERROR, - model.Job.table.c.state == model.Job.states.DELETED ) ), - self.model_class.table.c.create_time >= start_date, - self.model_class.table.c.create_time < end_date ) ) + return trans.sa_session.query( self.model_class ) \ + .filter( and_( not_( or_( model.Job.table.c.state == model.Job.states.OK, + model.Job.table.c.state == model.Job.states.ERROR, + model.Job.table.c.state == model.Job.states.DELETED ) ), + self.model_class.table.c.create_time >= start_date, + self.model_class.table.c.create_time < end_date ) ) \ + .enable_eagerloads( False ) class UserForMonthListGrid( SpecifiedDateListGrid ): def build_initial_query( self, trans, **kwd ): email = util.restore_text( kwd.get( 'email', '' ) ) - year, month = map( int, kwd.get( 'month', datetime.utcnow().strftime( "%Y-%m" ) ).split( "-" ) ) + # If specified_date is not received, we'll default to the current month + specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ) + specified_month = specified_date[ :7 ] + year, month = map( int, specified_month.split( "-" ) ) start_date = date( year, month, 1 ) end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] ) return trans.sa_session.query( model.Job ) \ @@ -127,19 +141,22 @@ class UserForMonthListGrid( SpecifiedDat model.User.table.c.email == email, model.Job.table.c.create_time >= start_date, model.Job.table.c.create_time < end_date ) ) \ - .order_by( desc( model.Job.table.c.create_time ) ) + .enable_eagerloads( False ) class ToolForMonthListGrid( SpecifiedDateListGrid ): def build_initial_query( self, trans, **kwd ): + # If specified_date is not received, we'll default to the current month + specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ) + specified_month = specified_date[ :7 ] tool_id = util.restore_text( kwd.get( 'tool_id', '' ) ) - year, month = map( int, kwd.get( 'month', datetime.utcnow().strftime( "%Y-%m" ) ).split( "-" ) ) + year, month = map( int, specified_month.split( "-" ) ) start_date = date( year, month, 1 ) end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] ) - return trans.sa_session.query( model.Job ) \ - .filter( and_( model.Job.table.c.tool_id == tool_id, - model.Job.table.c.create_time >= start_date, - model.Job.table.c.create_time < end_date ) ) \ - .order_by( desc( model.Job.table.c.create_time ) ) + return trans.sa_session.query( self.model_class ) \ + .filter( and_( self.model_class.table.c.tool_id == tool_id, + self.model_class.table.c.create_time >= start_date, + self.model_class.table.c.create_time < end_date ) ) \ + .enable_eagerloads( False ) class Jobs( BaseController ): @@ -158,8 +175,7 @@ class Jobs( BaseController ): action='job_info', **kwd ) ) if operation == "tool_per_month": - # The received id is the job id, so we need to get the id of the user - # that submitted the job. + # The received id is the job id, so we need to get the jobs tool_id. job_id = kwd.get( 'id', None ) job = get_job( trans, job_id ) kwd[ 'tool_id' ] = job.tool_id @@ -194,8 +210,7 @@ class Jobs( BaseController ): action='job_info', **kwd ) ) if operation == "tool_per_month": - # The received id is the job id, so we need to get the id of the user - # that submitted the job. + # The received id is the job id, so we need to get the jobs tool_id. job_id = kwd.get( 'id', None ) job = get_job( trans, job_id ) kwd[ 'tool_id' ] = job.tool_id @@ -222,7 +237,10 @@ class Jobs( BaseController ): params = util.Params( kwd ) message = '' monitor_email = params.get( 'monitor_email', 'monitor(a)bx.psu.edu' ) - year, month = map( int, params.get( 'month', datetime.utcnow().strftime( "%Y-%m" ) ).split( "-" ) ) + # If specified_date is not received, we'll default to the current month + specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ) + specified_month = specified_date[ :7 ] + year, month = map( int, specified_month.split( "-" ) ) start_date = date( year, month, 1 ) end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] ) month_label = start_date.strftime( "%B" ) @@ -254,7 +272,10 @@ class Jobs( BaseController ): def specified_month_in_error( self, trans, **kwd ): params = util.Params( kwd ) message = '' - year, month = map( int, params.get( 'month', datetime.utcnow().strftime( "%Y-%m" ) ).split( "-" ) ) + # If specified_date is not received, we'll default to the current month + specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ) + specified_month = specified_date[ :7 ] + year, month = map( int, specified_month.split( "-" ) ) start_date = date( year, month, 1 ) end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] ) month_label = start_date.strftime( "%B" ) @@ -289,8 +310,7 @@ class Jobs( BaseController ): action='job_info', **kwd ) ) if operation == "tool_per_month": - # The received id is the job id, so we need to get the id of the user - # that submitted the job. + # The received id is the job id, so we need to get the jobs tool_id. job_id = kwd.get( 'id', None ) job = get_job( trans, job_id ) kwd[ 'tool_id' ] = job.tool_id @@ -332,7 +352,9 @@ class Jobs( BaseController ): row.total_jobs, row.date.strftime( "%B" ), row.date.strftime( "%Y" ) ) ) - return trans.fill_template( '/webapps/reports/jobs_per_month_all.mako', jobs=jobs, message=message ) + return trans.fill_template( '/webapps/reports/jobs_per_month_all.mako', + jobs=jobs, + message=message ) @web.expose def per_month_in_error( self, trans, **kwd ): params = util.Params( kwd ) @@ -349,7 +371,9 @@ class Jobs( BaseController ): row.total_jobs, row.date.strftime( "%B" ), row.date.strftime( "%Y" ) ) ) - return trans.fill_template( '/webapps/reports/jobs_per_month_in_error.mako', jobs=jobs, message=message ) + return trans.fill_template( '/webapps/reports/jobs_per_month_in_error.mako', + jobs=jobs, + message=message ) @web.expose def per_user( self, trans, **kwd ): params = util.Params( kwd ) @@ -398,8 +422,7 @@ class Jobs( BaseController ): action='job_info', **kwd ) ) if operation == "tool_per_month": - # The received id is the job id, so we need to get the id of the user - # that submitted the job. + # The received id is the job id, so we need to get the jobs tool_id. job_id = kwd.get( 'id', None ) job = get_job( trans, job_id ) kwd[ 'tool_id' ] = job.tool_id @@ -434,12 +457,15 @@ class Jobs( BaseController ): for row in q.execute(): jobs.append( ( row.tool_id, row.total_jobs ) ) - return trans.fill_template( '/webapps/reports/jobs_per_tool.mako', jobs=jobs, message=message ) + return trans.fill_template( '/webapps/reports/jobs_per_tool.mako', + jobs=jobs, + message=message ) @web.expose def tool_per_month( self, trans, **kwd ): params = util.Params( kwd ) message = '' tool_id = params.get( 'tool_id', 'Add a column1' ) + specified_date = params.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ) q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ).label( 'date' ), sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), whereclause = model.Job.table.c.tool_id == tool_id, @@ -452,7 +478,11 @@ class Jobs( BaseController ): row.total_jobs, row.date.strftime( "%B" ), row.date.strftime( "%Y" ) ) ) - return trans.fill_template( '/webapps/reports/jobs_tool_per_month.mako', tool_id=tool_id, jobs=jobs, message=message ) + return trans.fill_template( '/webapps/reports/jobs_tool_per_month.mako', + specified_date=specified_date, + tool_id=tool_id, + jobs=jobs, + message=message ) @web.expose def tool_for_month( self, trans, **kwd ): if 'operation' in kwd: @@ -462,8 +492,7 @@ class Jobs( BaseController ): action='job_info', **kwd ) ) if operation == "tool_per_month": - # The received id is the job id, so we need to get the id of the user - # that submitted the job. + # The received id is the job id, so we need to get the jobs tool_id. job_id = kwd.get( 'id', None ) job = get_job( trans, job_id ) kwd[ 'tool_id' ] = job.tool_id @@ -497,7 +526,10 @@ class Jobs( BaseController ): .one() # TODO: for some reason the job_info.id is not the same as job_id in the template, so we need to pass job_id # This needs to be fixed ASAP! - return trans.fill_template( '/webapps/reports/job_info.mako', job_id=job_id, job_info=job_info, message=message ) + return trans.fill_template( '/webapps/reports/job_info.mako', + job_id=job_id, + job_info=job_info, + message=message ) @web.expose def per_domain( self, trans, **kwd ): # TODO: rewrite using alchemy --- a/templates/webapps/reports/system.mako +++ b/templates/webapps/reports/system.mako @@ -1,13 +1,17 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> +<% + from galaxy.web.framework.helpers import time_ago +%> + %if message: ${render_msg( message, 'done' )} %endif <div class="toolForm"><h3 align="center">Old Histories and Datasets</h3> - <table align="center" width="70%" class="border" cellpadding="5" cellspacing="5"> + <table align="center" width="90%" class="border" cellpadding="5" cellspacing="5"><tr><td><form method="post" action="system"> @@ -33,10 +37,14 @@ </td></tr></table> - <br clear="left" /><br /> + <br clear="left" /><h3 align="center">Current Disk Space Where Datasets are Stored</h3> - <table align="center" width="60%" class="colored"> - <tr><td colspan="5"><div class="toolFormTitle">Disk Usage for ${file_path}</div></td></tr> + <table align="center" width="90%" class="colored"> + <tr> + <td colspan="5"> + <b>Disk Usage for ${file_path}</b> + </td> + </tr><tr class="header"><td>File System</td><td>Disk Size</td> @@ -51,16 +59,16 @@ <td>${disk_usage[3]}</td><td>${disk_usage[4]}</td></tr> - %if len( datasets ) == 0: - <tr class="header"><td colspan="5">There are no datasets larger than ${file_size_str}</td></tr> - %else: - <tr><td colspan="5"><div class="toolFormTitle">${len( datasets )} largest datasets over ${file_size_str}</div></td></tr> + </table> + <br clear="left" /> + %if datasets.count() > 0: + <h3 align="center">${datasets.count()} largest unpurged data files over ${file_size_str}</h3> + <table align="center" width="90%" class="colored"><tr class="header"><td>File</td><td>Last Updated</td> - <td>History ID</td><td>Deleted</td> - <td>Size on Disk</td> + <td>File Size</td></tr><% ctr = 0 %> %for dataset in datasets: @@ -69,14 +77,19 @@ %else: <tr class="tr"> %endif - <td>dataset_${dataset[0]}.dat</td> - <td>${dataset[1]}</td> - <td>${dataset[2]}</td> - <td>${dataset[3]}</td> - <td>${dataset[4]}</td> + <td> + <% dataset_label = 'dataset%d_.dat' % dataset.id %> + <a href="${h.url_for( controller='system', action='dataset_info', id=trans.security.encode_id( dataset.id ) )}">${dataset_label}</a> + </td> + <td>${time_ago( dataset.update_time )}</td> + <td>${dataset.deleted}</td> + <td>${dataset.file_size}</td></tr><% ctr += 1 %> %endfor - %endif - </table> + </table> + <br clear="left" /> + %else: + <h3 align="center">There are no unpurged data files larger than ${file_size_str}</h3> + %endif </div> --- /dev/null +++ b/templates/webapps/reports/dataset_info.mako @@ -0,0 +1,119 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<% + from galaxy.web.framework.helpers import time_ago + from galaxy.web.controllers.library_common import get_containing_library_from_library_dataset +%> + +%if message: + ${render_msg( message, 'done' )} +%endif + +<div class="toolForm"> + <h3 align="center">Dataset Information</h3> + <div class="toolFormBody"> + <div class="form-row"> + <label>Date uploaded:</label> + ${time_ago( dataset.create_time )} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Last updated:</label> + ${time_ago( dataset.update_time )} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>File size:</label> + ${dataset.get_size( nice_size=True )} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>State:</label> + ${dataset.state} + <div style="clear: both"></div> + </div> + </div> +</div> +%if associated_hdas: + <p/> + <b>Active (undeleted) history items that use this library dataset's disk file</b> + <div class="toolForm"> + <table class="grid"> + <thead> + <tr> + <th>History</th> + <th>History Item</th> + <th>Last Updated</th> + <th>User</th> + </tr> + </thead> + %for hda in associated_hdas: + <tr> + <td>${hda.history.get_display_name()}</td> + <td>${hda.get_display_name()}</td> + <td>${time_ago( hda.update_time )}</td> + <td> + %if hda.history.user: + ${hda.history.user.email} + %else: + anonymous + %endif + </td> + </tr> + %endfor + </table> + </div> + <p/> +%endif +%if associated_lddas: + <p/> + <b>Other active (undeleted) library datasets that use this library dataset's disk file</b> + <div class="toolForm"> + <table class="grid"> + <thead> + <tr> + <th>Library</th> + <th>Folder</th> + <th>Library Dataset</th> + <th>Last Updated</th> + <th>Uploaded By</th> + </tr> + </thead> + %for ldda in associated_lddas: + <% containing_library = get_containing_library_from_library_dataset( trans, ldda.library_dataset ) %> + <tr> + <td> + <% + if containing_library: + library_display_name = containing_library.get_display_name() + else: + library_display_name = 'error finding library' + %> + ${library_display_name} + </td> + <td> + <% + library_dataset = ldda.library_dataset + folder = library_dataset.folder + folder_display_name = folder.get_display_name() + if folder_display_name == library_display_name: + folder_display_name = 'library root' + %> + ${folder_display_name} + </td> + <td>${ldda.get_display_name()}</td> + <td>${time_ago( ldda.update_time )}</td> + <td> + %if ldda.user: + ${ldda.user.email} + %else: + anonymous + %endif + </td> + </tr> + %endfor + </table> + </div> + <p/> +%endif --- a/templates/webapps/reports/jobs_per_user.mako +++ b/templates/webapps/reports/jobs_per_user.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -432,13 +432,19 @@ class Dataset( object ): path = os.path.join( os.path.join( self.file_path, *directory_hash_id( self.id ) ), "dataset_%d_files" % self.id ) # Make path absolute return os.path.abspath( path ) - def get_size( self ): + def get_size( self, nice_size=False ): """Returns the size of the data on disk""" if self.file_size: - return self.file_size + if nice_size: + return galaxy.datatypes.data.nice_size( self.file_size ) + else: + return self.file_size else: try: - return os.path.getsize( self.file_name ) + if nice_size: + return galaxy.datatypes.data.nice_size( os.path.getsize( self.file_name ) ) + else: + return os.path.getsize( self.file_name ) except OSError: return 0 def set_size( self ): --- a/templates/webapps/reports/jobs_specified_month_in_error.mako +++ b/templates/webapps/reports/jobs_specified_month_in_error.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> --- a/templates/webapps/reports/jobs_per_tool.mako +++ b/templates/webapps/reports/jobs_per_tool.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> --- a/templates/webapps/reports/users_last_access_date.mako +++ b/templates/webapps/reports/users_last_access_date.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> --- a/templates/webapps/reports/jobs_per_month_in_error.mako +++ b/templates/webapps/reports/jobs_per_month_in_error.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> @@ -24,7 +24,7 @@ %else: <tr class="tr"> %endif - <td><a href="${h.url_for( controller='jobs', action='specified_month_in_error', month=job[0] )}">${job[2]} ${job[3]}</a></td> + <td><a href="${h.url_for( controller='jobs', action='specified_month_in_error', specified_date=job[0]+'-01' )}">${job[2]} ${job[3]}</a></td><td>${job[1]}</td></tr><% ctr += 1 %> --- a/lib/galaxy/webapps/reports/controllers/system.py +++ b/lib/galaxy/webapps/reports/controllers/system.py @@ -1,10 +1,6 @@ import operator, os from datetime import datetime, timedelta from galaxy.web.base.controller import * -#import pkg_resources -#pkg_resources.require( "SQLAlchemy >= 0.4" ) -#from sqlalchemy.orm import eagerload -#from sqlalchemy import desc from galaxy import model from galaxy.model.orm import * import logging @@ -44,7 +40,6 @@ class System( BaseController ): deleted_histories_days=deleted_histories_days, deleted_datasets_days=deleted_datasets_days, message=message ) - def userless_histories( self, trans, **kwd ): """The number of userless histories and associated datasets that have not been updated for the specified number of days.""" params = util.Params( kwd ) @@ -54,11 +49,6 @@ class System( BaseController ): cutoff_time = datetime.utcnow() - timedelta( days=userless_histories_days ) history_count = 0 dataset_count = 0 - #h = self.app.model.History - #where = ( h.table.c.user_id==None ) & ( h.table.c.deleted=='f' ) & ( h.table.c.update_time < cutoff_time ) - #histories = h.query().filter( where ).options( eagerload( 'datasets' ) ) - - #for history in histories: for history in trans.sa_session.query( model.History ) \ .filter( and_( model.History.table.c.user_id == None, model.History.table.c.deleted == True, @@ -71,7 +61,6 @@ class System( BaseController ): else: message = "Enter the number of days." return str( userless_histories_days ), message - def deleted_histories( self, trans, **kwd ): """ The number of histories that were deleted more than the specified number of days ago, but have not yet been purged. @@ -104,7 +93,6 @@ class System( BaseController ): else: message = "Enter the number of days." return str( deleted_histories_days ), message - def deleted_datasets( self, trans, **kwd ): """The number of datasets that were deleted more than the specified number of days ago, but have not yet been purged.""" params = util.Params( kwd ) @@ -128,6 +116,25 @@ class System( BaseController ): else: message = "Enter the number of days." return str( deleted_datasets_days ), message + @web.expose + def dataset_info( self, trans, **kwd ): + params = util.Params( kwd ) + message = '' + dataset = trans.sa_session.query( model.Dataset ).get( trans.security.decode_id( kwd.get( 'id', '' ) ) ) + # Get all associated hdas and lddas that use the same disk file. + associated_hdas = trans.sa_session.query( trans.model.HistoryDatasetAssociation ) \ + .filter( and_( trans.model.HistoryDatasetAssociation.deleted == False, + trans.model.HistoryDatasetAssociation.dataset_id == dataset.id ) ) \ + .all() + associated_lddas = trans.sa_session.query( trans.model.LibraryDatasetDatasetAssociation ) \ + .filter( and_( trans.model.LibraryDatasetDatasetAssociation.deleted == False, + trans.model.LibraryDatasetDatasetAssociation.dataset_id == dataset.id ) ) \ + .all() + return trans.fill_template( '/webapps/reports/dataset_info.mako', + dataset=dataset, + associated_hdas=associated_hdas, + associated_lddas=associated_lddas, + message=message ) def get_disk_usage( self, file_path ): df_cmd = 'df -h ' + file_path is_sym_link = os.path.islink( file_path ) @@ -163,13 +170,13 @@ class System( BaseController ): def disk_usage( self, trans, **kwd ): file_path = trans.app.config.file_path disk_usage = self.get_disk_usage( file_path ) - min_file_size = 2**32 # 4 Gb + #min_file_size = 2**32 # 4 Gb + min_file_size = 0 file_size_str = nice_size( min_file_size ) - datasets = [] - for dataset in trans.sa_session.query( model.Dataset ) \ - .filter( model.Dataset.table.c.file_size > min_file_size ) \ - .order_by( desc( model.Dataset.table.c.file_size ) ): - datasets.append( ( dataset.id, str( dataset.update_time )[0:10], dataset.history.history_id, dataset.deleted, dataset.file_size ) ) + datasets = trans.sa_session.query( model.Dataset ) \ + .filter( and_( model.Dataset.table.c.purged == False, + model.Dataset.table.c.file_size > min_file_size ) ) \ + .order_by( desc( model.Dataset.table.c.file_size ) ) return file_path, disk_usage, datasets, file_size_str def nice_size( size ): --- a/lib/galaxy/webapps/reports/controllers/users.py +++ b/lib/galaxy/webapps/reports/controllers/users.py @@ -13,14 +13,12 @@ log = logging.getLogger( __name__ ) class Users( BaseController ): @web.expose def registered_users( self, trans, **kwd ): - params = util.Params( kwd ) - message = params.get( 'message', '' ) + message = util.restore_text( kwd.get( 'message', '' ) ) num_users = trans.sa_session.query( galaxy.model.User ).count() return trans.fill_template( '/webapps/reports/registered_users.mako', num_users=num_users, message=message ) @web.expose def registered_users_per_month( self, trans, **kwd ): - params = util.Params( kwd ) - message = params.get( 'message', '' ) + message = util.restore_text( kwd.get( 'message', '' ) ) q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( galaxy.model.User.table.c.create_time ) ).label( 'date' ), sa.func.count( galaxy.model.User.table.c.id ).label( 'num_users' ) ), from_obj = [ galaxy.model.User.table ], @@ -29,15 +27,19 @@ class Users( BaseController ): users = [] for row in q.execute(): users.append( ( row.date.strftime( "%Y-%m" ), - row.num_users, - row.date.strftime( "%B" ), - row.date.strftime( "%Y" ) ) ) - return trans.fill_template( '/webapps/reports/registered_users_per_month.mako', users=users, message=message ) + row.num_users, + row.date.strftime( "%B" ), + row.date.strftime( "%Y" ) ) ) + return trans.fill_template( '/webapps/reports/registered_users_per_month.mako', + users=users, + message=message ) @web.expose def specified_month( self, trans, **kwd ): - params = util.Params( kwd ) - message = params.get( 'message', '' ) - year, month = map( int, params.get( 'month', datetime.utcnow().strftime( "%Y-%m" ) ).split( "-" ) ) + message = util.restore_text( kwd.get( 'message', '' ) ) + # If specified_date is not received, we'll default to the current month + specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ) + specified_month = specified_date[ :7 ] + year, month = map( int, specified_month.split( "-" ) ) start_date = date( year, month, 1 ) end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] ) month_label = start_date.strftime( "%B" ) @@ -63,9 +65,10 @@ class Users( BaseController ): message=message ) @web.expose def specified_date( self, trans, **kwd ): - params = util.Params( kwd ) - message = params.get( 'message', '' ) - year, month, day = map( int, params.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ).split( "-" ) ) + message = util.restore_text( kwd.get( 'message', '' ) ) + # If specified_date is not received, we'll default to the current month + specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ) + year, month, day = map( int, specified_date.split( "-" ) ) start_date = date( year, month, day ) end_date = start_date + timedelta( days=1 ) day_of_month = start_date.strftime( "%d" ) @@ -91,9 +94,8 @@ class Users( BaseController ): message=message ) @web.expose def last_access_date( self, trans, **kwd ): - params = util.Params( kwd ) - message = params.get( 'message', '' ) - not_logged_in_for_days = params.get( 'not_logged_in_for_days', 90 ) + message = util.restore_text( kwd.get( 'message', '' ) ) + not_logged_in_for_days = kwd.get( 'not_logged_in_for_days', 90 ) if not not_logged_in_for_days: not_logged_in_for_days = 0 cutoff_time = datetime.utcnow() - timedelta( days=int( not_logged_in_for_days ) ) --- a/templates/webapps/reports/registered_users_specified_month.mako +++ b/templates/webapps/reports/registered_users_specified_month.mako @@ -24,7 +24,7 @@ %else: <tr class="tr"> %endif - <td><a href="${h.url_for( controller='users', action='specified_date', specified_date=user[0], day_label=user[3], month_label=month_label, year_label=year_label, day_of_month=user[1] )}">${user[3]}, ${month_label} ${user[1]}, ${year_label}</a></td> + <td><a href="${h.url_for( controller='users', action='specified_date', specified_date=user[0] )}">${user[3]}, ${month_label} ${user[1]}, ${year_label}</a></td><td>${user[2]}</td></tr><% ctr += 1 %> --- a/templates/webapps/reports/index.mako +++ b/templates/webapps/reports/index.mako @@ -73,14 +73,14 @@ </div><div class="toolSectionBody"><div class="toolSectionBg"> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='today_all' )}">Number of jobs today</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='specified_month_all' )}">Number of jobs per day for current month</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='specified_month_in_error' )}">Number of jobs in error per day for current month</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='today_all' )}">Today's jobs</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='specified_month_all' )}">Jobs per day this month</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='specified_month_in_error' )}">Jobs in error per day this month</a></div><div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='all_unfinished' )}">All unfinished jobs</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_month_all' )}">Number of jobs per month</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_month_in_error' )}">Number of jobs in error per month</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_user' )}">Number of jobs per user</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_tool' )}">Number of jobs per tool</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_month_all' )}">Jobs per month</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_month_in_error' )}">Jobs in error per month</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_user' )}">Jobs per user</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_tool' )}">Jobs per tool</a></div></div></div><div class="toolSectionPad"></div> @@ -101,7 +101,7 @@ </div><div class="toolSectionBody"><div class="toolSectionBg"> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='system', action='index' )}">Disk space, old histories and datasets</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='system', action='index' )}">Disk space maintenance</a></div></div></div></div> @@ -110,6 +110,6 @@ </%def><%def name="center_panel()"> - <% center_url = h.url_for( controller='jobs', action='today_all' ) %> + <% center_url = h.url_for( controller='jobs', action='specified_month_all' ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def> --- a/templates/webapps/reports/jobs_per_domain.mako +++ b/templates/webapps/reports/jobs_per_domain.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -1904,15 +1904,14 @@ def branch_deleted( folder ): def get_containing_library_from_library_dataset( trans, library_dataset ): """Given a library_dataset, get the containing library""" folder = library_dataset.folder - parent = folder while folder.parent: - parent = folder.parent - # We have parent set to the library's root folder, which has the - # same name as the library + folder = folder.parent + # We have folder set to the library's root folder, which has the same name as the library for library in trans.sa_session.query( trans.model.Library ) \ .filter( and_( trans.model.Library.table.c.deleted == False, - trans.model.Library.table.c.name == parent.name ) ): - if library.root_folder == parent: + trans.model.Library.table.c.name == folder.name ) ): + # Just to double-check + if library.root_folder == folder: return library return None --- a/templates/webapps/reports/jobs_tool_per_month.mako +++ b/templates/webapps/reports/jobs_tool_per_month.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> @@ -25,7 +25,7 @@ <tr class="tr"> %endif <td>${job[2]} ${job[3]}</td> - <td><a href="${h.url_for( controller='jobs', action='tool_for_month', tool_id=tool_id, month=job[0] )}">${job[1]}</a></td> + <td><a href="${h.url_for( controller='jobs', action='tool_for_month', tool_id=tool_id, specified_date=job[0]+'-01' )}">${job[1]}</a></td></tr><% ctr += 1 %> %endfor --- a/templates/webapps/reports/registered_users_per_month.mako +++ b/templates/webapps/reports/registered_users_per_month.mako @@ -24,7 +24,7 @@ %else: <tr class="tr"> %endif - <td><a href="${h.url_for( controller='users', action='specified_month', month=user[0], month_label=user[2].strip(), year_label=user[3] )}">${user[2]} ${user[3]}</a></td> + <td><a href="${h.url_for( controller='users', action='specified_month', specified_date=user[0]+'-01' )}">${user[2]} ${user[3]}</a></td><td>${user[1]}</td></tr><% ctr += 1 %> --- a/templates/webapps/reports/jobs_specified_month_all.mako +++ b/templates/webapps/reports/jobs_specified_month_all.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> --- a/templates/webapps/reports/jobs_per_month_all.mako +++ b/templates/webapps/reports/jobs_per_month_all.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> %if message: - ${render_msg( message, status )} + ${render_msg( message, 'done' )} %endif <div class="toolForm"> @@ -26,7 +26,7 @@ %else: <tr class="tr"> %endif - <td><a href="${h.url_for( controller='jobs', action='specified_month_all', month=job[0] )}">${job[4]} ${job[5]}</a></td> + <td><a href="${h.url_for( controller='jobs', action='specified_month_all', specified_date=job[0]+'-01' )}">${job[4]} ${job[5]}</a></td><td>${job[1]}</td><td>${job[2]}</td><td>${job[3]}</td>

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galaxy-dist commit f0c8355714e2: Update cufflinks wrapper and tests. Expression output files are now tabular and all outputs are evaluated in functional test.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '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 1275657576 14400 # Node ID f0c8355714e2b1fc1f70026485a4b24843609b2a # Parent e924fd0ed0174300161577c30936c649d2cd2d08 Update cufflinks wrapper and tests. Expression output files are now tabular and all outputs are evaluated in functional test. --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -50,12 +50,15 @@ </inputs><outputs> - <data format="expr" name="genes_expression" label="${tool.name} on ${on_string}: gene expression"/> - <data format="expr" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression"/> + <data format="tabular" name="genes_expression" label="${tool.name} on ${on_string}: gene expression"/> + <data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression"/><data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts"/></outputs><tests> + <test><param name="sPaired" value="single"/><param name="input" value="cufflinks_in.sam"/> @@ -65,12 +68,9 @@ <param name="pre_mrna_fraction" value="0.05"/><param name="min_map_quality" value="0"/><param name="use_ref" value="No"/> - <output name="assembled_isoforms" file="cufflinks_out1.gtf"/> -  + <output name="assembled_isoforms" file="cufflinks_out1.gtf"/></test></tests>

1 0

galaxy-dist commit d01207f24908: Add a temporary fix to grid_common.mako, eliminating the use of the categorical-filter style for grid StateColumns so that the request will not be mangled before it reaches the server. Added several TODOs in the grid Javascript code outlining the problem.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '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 1275671670 14400 # Node ID d01207f24908bc3f6d5323689f0aa46557f4d254 # Parent d285c65c66d3d49f3ddd998fe2d28b60996581f1 Add a temporary fix to grid_common.mako, eliminating the use of the categorical-filter style for grid StateColumns so that the request will not be mangled before it reaches the server. Added several TODOs in the grid Javascript code outlining the problem. --- a/templates/grid_common.mako +++ b/templates/grid_common.mako @@ -1,5 +1,5 @@ <%! - from galaxy.web.framework.helpers.grids import TextColumn, GridColumnFilter + from galaxy.web.framework.helpers.grids import TextColumn, StateColumn, GridColumnFilter from galaxy.web.framework.helpers import iff %> @@ -15,81 +15,110 @@ <td align="left" style="padding-left: 10px">${column_label}:</td> %endif <td> - %if isinstance(column, TextColumn): - <form class="text-filter-form" column_key="${column.key}" action="${url( dict() )}" method="get" > - ## Carry forward filtering criteria with hidden inputs. - %for temp_column in grid.columns: - %if temp_column.key in cur_filter_dict: - <% value = cur_filter_dict[ temp_column.key ] %> - %if value != "All": + %if isinstance(column, TextColumn): + <form class="text-filter-form" column_key="${column.key}" action="${url( dict() )}" method="get" > + ## Carry forward filtering criteria with hidden inputs. + %for temp_column in grid.columns: + %if temp_column.key in cur_filter_dict: + <% value = cur_filter_dict[ temp_column.key ] %> + %if value != "All": + <% + if isinstance( temp_column, TextColumn ): + value = h.to_json_string( value ) + %> + <input type="hidden" id="${temp_column.key}" name="f-${temp_column.key}" value='${value}'/> + %endif + %endif + %endfor + + ## Print current filtering criteria and links to delete. + <span id="${column.key}-filtering-criteria"> + %if column.key in cur_filter_dict: + <% column_filter = cur_filter_dict[column.key] %> + %if isinstance( column_filter, basestring ): + %if column_filter != "All": + <span class='text-filter-val'> + ${cur_filter_dict[column.key]} + <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> + <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + </span> + %endif + %elif isinstance( column_filter, list ): + %for i, filter in enumerate( column_filter ): + %if i > 0: + , + %endif + <span class='text-filter-val'>${filter} + <% + new_filter = list( column_filter ) + del new_filter[ i ] + new_column_filter = GridColumnFilter( "", { column.key : h.to_json_string( new_filter ) } ) + %> + <a href="${url( new_column_filter.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + </span> + %endfor + %endif + %endif + </span> + ## Print input field for column. + <span> + <% value = iff( column.filterable == "standard", column.label.lower(), "") %> + <input class="no-padding-or-margin" id="input-${column.key}-filter" name="f-${column.key}" type="text" value="${value}" size="15"/> + <input class='submit-image' type='image' src='${h.url_for('/static/images/mag_glass.png')}' alt='Filter'/> + </span> + </form> + ###################### + ## TODO: eliminate this elif condition when the categorical-filter style in grid_common.mako is fixed to that it no + ## longer mangles the request by eliminating parameters from it before it reaches the server. Since the categorical-filter + ## style is not used here, paging will not work... + ###################### + %elif isinstance( column, StateColumn ): + kwargs: ${kwargs}<br/> + <span id="${column.key}-filtering-criteria"> + %for i, filter in enumerate( column.get_accepted_filters() ): + <% + # HACK: we know that each filter will have only a single argument, so get that single argument. + for key, arg in filter.args.items(): + filter_key = key + filter_arg = arg + %> + %if i > 0: + | + %endif + %if column.key in cur_filter_dict and column.key in filter.args and cur_filter_dict[column.key] == filter.args[column.key]: + <span class="categorical-filter ${column.key}-filter current-filter">${filter.label}</span> + %else: <% - if isinstance( temp_column, TextColumn ): - value = h.to_json_string( value ) + my_dict = {} + my_dict.update( kwargs ) + my_dict.update( filter.get_url_args() ) %> - <input type="hidden" id="${temp_column.key}" name="f-${temp_column.key}" value='${value}'/> + <a href="${url( my_dict )}" filter_key="${filter_key}" filter_val="${filter_arg}">${filter.label}</a> %endif - %endif - %endfor - - ## Print current filtering criteria and links to delete. + %endfor + </span> + %else: <span id="${column.key}-filtering-criteria"> - %if column.key in cur_filter_dict: - <% column_filter = cur_filter_dict[column.key] %> - %if isinstance( column_filter, basestring ): - %if column_filter != "All": - <span class='text-filter-val'> - ${cur_filter_dict[column.key]} - <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> - <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + %for i, filter in enumerate( column.get_accepted_filters() ): + <% + # HACK: we know that each filter will have only a single argument, so get that single argument. + for key, arg in filter.args.items(): + filter_key = key + filter_arg = arg + %> + %if i > 0: + | + %endif + %if column.key in cur_filter_dict and column.key in filter.args and cur_filter_dict[column.key] == filter.args[column.key]: + <span class="categorical-filter ${column.key}-filter current-filter">${filter.label}</span> + %else: + <span class="categorical-filter ${column.key}-filter"> + <a href="${url( filter.get_url_args() )}" filter_key="${filter_key}" filter_val="${filter_arg}">${filter.label}</a></span> %endif - %elif isinstance( column_filter, list ): - %for i, filter in enumerate( column_filter ): - %if i > 0: - , - %endif - <span class='text-filter-val'>${filter} - <% - new_filter = list( column_filter ) - del new_filter[ i ] - new_column_filter = GridColumnFilter( "", { column.key : h.to_json_string( new_filter ) } ) - %> - <a href="${url( new_column_filter.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> - </span> - %endfor - - %endif - %endif + %endfor </span> - ## Print input field for column. - <span> - <% value = iff( column.filterable == "standard", column.label.lower(), "") %> - <input class="no-padding-or-margin" id="input-${column.key}-filter" name="f-${column.key}" type="text" value="${value}" size="15"/> - <input class='submit-image' type='image' src='${h.url_for('/static/images/mag_glass.png')}' alt='Filter'/> - </span> - </form> - %else: - <span id="${column.key}-filtering-criteria"> - %for i, filter in enumerate( column.get_accepted_filters() ): - <% - # HACK: we know that each filter will have only a single argument, so get that single argument. - for key, arg in filter.args.items(): - filter_key = key - filter_arg = arg - %> - %if i > 0: - | - %endif - %if column.key in cur_filter_dict and column.key in filter.args and cur_filter_dict[column.key] == filter.args[column.key]: - <span class="categorical-filter ${column.key}-filter current-filter">${filter.label}</span> - %else: - <span class="categorical-filter ${column.key}-filter"> - <a href="${url( filter.get_url_args() )}" filter_key="${filter_key}" filter_val="${filter_arg}">${filter.label}</a> - </span> - %endif - %endfor - </span> - %endif + %endif </td></tr></%def> --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -161,6 +161,16 @@ }); // Initialize categorical filters. + // #################### + // TODO: This style is used in grid_common.mako to wrap the links created for certain GridColumn + // subclasses ( e.g., DeletedColumn, StateColumn, etc ) where the link labels are generated in the + // class's get_accepted_filters() method. The problem is that when the link is clicked, this style + // will eliminate all request parameters except for those that are included in the cur_filter_dict + // dictionary that is used to build the url_args variable in this template. This process needs to + // be corrected so that the only changes made to the request are updating the values of parameters + // in the request with the new values obtained from cur_filter_dict, leaving all remaining request + // parameters alone. There is another related TODO in the set_categorical_filter() function below. + // #################### $('.categorical-filter > a').each( function() { $(this).click( function() { var filter_key = $(this).attr('filter_key'); @@ -397,6 +407,11 @@ } // Set new value for categorical filter. + // #################### + // TODO: this function mangles the initial request by eliminating many of the request parameters + // before calling update_grid(). This needs to be fixed - see the TODO in the categorical-filter + // style above. + // #################### function set_categorical_filter(name, new_value) { // Update filter hyperlinks to reflect new filter value. var category_filter = categorical_filters[name]; @@ -423,7 +438,7 @@ $(this).append(t); } }); - + // Update grid. url_args["f-" + name] = new_value; go_page_one(); @@ -498,7 +513,7 @@ var href_parms = href_parms_str.split("&"); var operation = null; var id = -1; - var webapp = 'galaxy' + var webapp = 'galaxy'; for (var index = 0; index < href_parms.length; index++) { if (href_parms[index].indexOf('operation') != -1) { // Found operation parm; get operation value.

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galaxy-dist commit f22b57fa537f: Filter datasets grid so that datasets in deleted histories are not shown.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '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 1275658986 14400 # Node ID f22b57fa537f9c2f3c458bf513bce2bd155239d1 # Parent f0c8355714e2b1fc1f70026485a4b24843609b2a Filter datasets grid so that datasets in deleted histories are not shown. --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -133,8 +133,9 @@ class HistoryDatasetAssociationListGrid( num_rows_per_page = 50 def apply_query_filter( self, trans, query, **kwargs ): # To filter HDAs by user, need to join HDA and History table and then filter histories by user. This is necessary because HDAs do not have - # a user relation. - return query.select_from( model.HistoryDatasetAssociation.table.join( model.History.table ) ).filter( model.History.user == trans.user ) + # a user relation. TODO: move the base of this query to build_initial_query. + # Summary: filter by user, and deleted==False for both dataset and history + return query.select_from( model.HistoryDatasetAssociation.table.join( model.History.table ) ).filter( model.History.user == trans.user ).filter( self.model_class.deleted==False ).filter( model.History.deleted==False) class DatasetInterface( BaseController, UsesAnnotations, UsesHistoryDatasetAssociation ):

1 0

galaxy-dist commit d285c65c66d3: BUGFIX: Removed console.logs from page and workflow editors.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannon.baker(a)emory.edu> # Date 1275663873 14400 # Node ID d285c65c66d3d49f3ddd998fe2d28b60996581f1 # Parent f22b57fa537f9c2f3c458bf513bce2bd155239d1 BUGFIX: Removed console.logs from page and workflow editors. --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -123,7 +123,7 @@ }); $(document).ajaxError( function ( e, x ) { - console.log( e, x ); + // console.log( e, x ); var message = x.responseText || x.statusText || "Could not connect to server"; show_modal( "Server error", message, { "Ignore error" : hide_modal } ); return false; --- a/templates/page/editor.mako +++ b/templates/page/editor.mako @@ -573,7 +573,7 @@ $(function(){ ## Generic error handling $(document).ajaxError( function ( e, x ) { - console.log( e, x ); + // console.log( e, x ); var message = x.responseText || x.statusText || "Could not connect to server"; show_modal( "Server error", message, { "Ignore error" : hide_modal } ); return false;

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galaxy-dist commit e924fd0ed017: trackster: Implemented drag-zooming by letting you drag a region in the top label track (where chrom position is shown). Refactored to not use zoom levels anymore.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '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 1275602338 14400 # Node ID e924fd0ed0174300161577c30936c649d2cd2d08 # Parent d25af565d085e19dccb8f20c857e633397e5da08 trackster: Implemented drag-zooming by letting you drag a region in the top label track (where chrom position is shown). Refactored to not use zoom levels anymore. --- a/static/welcome.html +++ b/static/welcome.html @@ -7,7 +7,7 @@ </head><body><div class="document"> - <div class="warningmessagelarge"> + <div class="donemessagelarge"><strong>Hello world! It's running...</strong><hr> To customize this page edit <code>static/welcome.html</code> --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -$(document).ready(function(){replace_big_select_inputs()});$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var 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",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="/static/images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="/static/images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="/static/images/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="/static/images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.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(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;this.zoom_factor=3;this.zoom_level= 0;this.track_id_counter=0;this.has_changes=false};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)]},update_options:function(){this.has_changes=true;var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];$("#viewport").append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a&&a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.center=this.center=(this.max_high-this.max_low)/2;this.zoom_level=0;$(".yaxislabel").remove()},redraw:function(f){this.span=this.max_high-this.max_low;var d=th is.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);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))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a,b){if(this.max_high===0||this.high-this.low<30){return}if(a){this.cente r=a/b.width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div />").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","30px");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.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(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.vi ew.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'></div>"),l=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(k),this.max_height=0;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a) ;this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.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 LineTrack=function(c,a,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_va lue}if(b.mode!==undefined){this.prefs.mode=b.mode}};$.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");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px",left:"10px"}) ;d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value, n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.prefs.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div />").addClass("form-row");var h="track_"+n+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),m=$("<input></input>").attr("id",h).val(b),k="track_ "+n+"_maxval",g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j),e="track_"+n+"_mode",d=$("<label></label>").attr("for",e).text("Display mode:"),i=(this.prefs.mode===undefined?"Line":this.prefs.mode),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Filled" id="mode_Filled">Filled</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+i).attr("selected","selected");return a.append(l).append(m).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.p refs.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(c,a,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}if(b.show_counts!==undefined){this.prefs.show_counts=b.show_counts}};$.ex tend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;a.mode="Auto";if(a.mode_div){a.mode_div.remove()}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},function(d){a.mode_div=$("<div class='right-float menubutton popup' />").text("Display Mode");a.header_div.append(a.mode_div);a.mode="Auto";var c=function(e){a.mode_div.text(e);a.mode=e;a.tile_cache.clear();a.draw()};make_popupmenu(a.mode_div,{Auto:function(){c("Auto")},Dense:function(){c("Dense")},Squish:function(){c("Squish")},Pack:function(){c("Pack")}});a.data_cache.set(b,d);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.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:fu nction(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===unde fined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,g,f,m,b,d,k,e,i){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>g){n.fillStyle=this.prefs.block_color;n.fillRect(k,i+1,e,9);n.fillStyle="#eee";for(var h=0,l=d.length;h<l;h++){if(b+h>=f&&b+h<=m){var a=Math.floor(Math.max(0,(b+h-f)*o));n.fillText(d[h],a+this.left_offset+j,i+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,i+4,e,3)}},draw_tile:function(X,h,n,al){var E=h*DENSITY*X,ad=(h+1)*DENSITY*X,D=DENSITY*X;var ae=E+"_"+ad;var z=this.data_cache.get(ae);if(z===undefined){this.data_queue[[E,ad]]=true;this.get_data(E,ad);return}var a=Math.ceil(D*al),L=$("<canvas class='tile'></canvas>"),Z=this.prefs.label_color,f=this.prefs.block_color,m=this.mode,V=(m==="Squish")||(m==="Dense")&&(m!=="Pack")||(m==="Auto"&&(z.extra_info==="no_detail")),P=this.left_offset,ak,s,a m;if(z.dataset_type==="summary_tree"){s=30}else{if(m==="Dense"){s=15;am=10}else{am=(V?this.vertical_nodetail_px:this.vertical_detail_px);s=this.incremental_slots(this.view.zoom_res,z.data,V,m)*am+15;ak=this.inc_slots[this.view.zoom_res]}}L.css({position:"absolute",top:0,left:(E-this.view.low)*al-P});L.get(0).width=a+P;L.get(0).height=s;n.parent().css("height",Math.max(this.height_px,s)+"px");var A=L.get(0).getContext("2d"),ai=A.measureText("A").width;A.fillStyle=f;A.font=this.default_font;A.textAlign="right";if(z.dataset_type=="summary_tree"){var K,H=55,ac=255-H,g=ac*2/3,R=z.data,C=z.max,l=z.avg;if(R.length>2){var b=Math.ceil((R[1][0]-R[0][0])*al)}else{var b=50}for(var ag=0,w=R.length;ag<w;ag++){var T=Math.ceil((R[ag][0]-E)*al);var S=R[ag][1];if(!S){continue}K=Math.floor(ac-(S/C)*ac);A.fillStyle="rgb("+K+","+K+","+K+")";A.fillRect(T+P,0,b,20);if(this.prefs.show_counts){if(K>g){A.fillStyle="black"}else{A.fillStyle="#ddd"}A.textAlign="center";A.fillText(R[ag][1],T+P+(b/2),12)} }n.append(L);return L}var aj=z.data;var af=0;for(var ag=0,w=aj.length;ag<w;ag++){var M=aj[ag],J=M[0],ah=M[1],U=M[2],F=M[3];if(ah<=ad&&U>=E){var W=Math.floor(Math.max(0,(ah-E)*al)),B=Math.ceil(Math.min(a,Math.max(0,(U-E)*al))),Q=(m==="Dense"?0:ak[J]*am);if(z.dataset_type==="bai"){A.fillStyle=f;if(M[4] instanceof Array){var t=Math.floor(Math.max(0,(M[4][0]-E)*al)),I=Math.ceil(Math.min(a,Math.max(0,(M[4][1]-E)*al))),r=Math.floor(Math.max(0,(M[5][0]-E)*al)),p=Math.ceil(Math.min(a,Math.max(0,(M[5][1]-E)*al)));if(M[4][1]>=E&&M[4][0]<=ad){this.rect_or_text(A,al,ai,E,ad,M[4][0],M[4][2],t+P,I-t,Q)}if(M[5][1]>=E&&M[5][0]<=ad){this.rect_or_text(A,al,ai,E,ad,M[5][0],M[5][2],r+P,p-r,Q)}if(r>I){A.fillStyle="#999";A.fillRect(I+P,Q+5,r-I,1)}}else{A.fillStyle=f;this.rect_or_text(A,al,ai,E,ad,ah,F,W+P,B-W,Q)}if(m!=="Dense"&&!V&&ah>E){A.fillStyle=this.prefs.label_color;if(h===0&&W-A.measureText(F).width<0){A.textAlign="left";A.fillText(J,B+2+P,Q+8)}else{A.textAlign="right";A.fillText(J,W-2+P,Q +8)}A.fillStyle=f}}else{if(z.dataset_type==="interval_index"){if(V){A.fillRect(W+P,Q+5,B-W,1)}else{var v=M[4],O=M[5],Y=M[6],e=M[7];var u,aa,G=null,an=null;if(O&&Y){G=Math.floor(Math.max(0,(O-E)*al));an=Math.ceil(Math.min(a,Math.max(0,(Y-E)*al)))}if(m!=="Dense"&&F!==undefined&&ah>E){A.fillStyle=Z;if(h===0&&W-A.measureText(F).width<0){A.textAlign="left";A.fillText(F,B+2+P,Q+8)}else{A.textAlign="right";A.fillText(F,W-2+P,Q+8)}A.fillStyle=f}if(e){if(v){if(v=="+"){A.fillStyle=RIGHT_STRAND}else{if(v=="-"){A.fillStyle=LEFT_STRAND}}A.fillRect(W+P,Q,B-W,10);A.fillStyle=f}for(var ae=0,d=e.length;ae<d;ae++){var o=e[ae],c=Math.floor(Math.max(0,(o[0]-E)*al)),N=Math.ceil(Math.min(a,Math.max((o[1]-E)*al)));if(c>N){continue}u=5;aa=3;A.fillRect(c+P,Q+aa,N-c,u);if(G!==undefined&&!(c>an||N<G)){u=9;aa=1;var ab=Math.max(c,G),q=Math.min(N,an);A.fillRect(ab+P,Q+aa,q-ab,u)}}}else{u=9;aa=1;A.fillRect(W+P,Q+aa,B-W,u);if(M.strand){if(M.strand=="+"){A.fillStyle=RIGHT_STRAND_INV}else{if(M.strand=="-"){A .fillStyle=LEFT_STRAND_INV}}A.fillRect(W+P,Q,B-W,10);A.fillStyle=prefs.block_color}}}}}af++}}n.append(L);return L},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(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("che cked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,b){FeatureTrack.call(this,c,a,b);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); +var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="/static/images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="/static/images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="/static/images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"r epeat")};var left_img_inv=new Image();left_img_inv.src="/static/images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.reset()};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_count er;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=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(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)]},update_options:function(){this.has_changes=true;var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];$("#viewport").append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a&&a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;$(".yaxislabel").remove()},redraw:function(f){var d=this.high-this.low,b=this.low,e=this.high;if(b<this.max_low){b=this.max_low}if(e>this.max_high){e=this.max_high}if(d<this.min_separation){e=b+this.min_separation}this.low=Math.floor(b);this.high=Math.ceil(e);this.resolution=Math.pow(10,Math.ceil(Math. log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/(this.max_high-this.max_low))*$("#overview-viewport").width(),width:Math.max(12,(this.high-this.low)/(this.max_high-this.max_low)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;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/c.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this. low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div />").addClass("track").append(this.header_div).append(this.content_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.content_div.css("height","30px");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");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;var k=$("<div style='position: relative;'></div>"),l=this.content_div.width()/f,h;thi s.content_div.children(":first").remove();this.content_div.append(k),this.max_height=0;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+l+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.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 LineTrack=function(c,a,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}if(b.mode!==undefined){this.prefs.mode=b.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_ran ge=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSIT Y*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.prefs.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}va r u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div />").addClass("form-row");var h="track_"+n+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),m=$("<input></input>").attr("id",h).val(b),k="track_"+n+"_maxval",g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val( j),e="track_"+n+"_mode",d=$("<label></label>").attr("for",e).text("Display mode:"),i=(this.prefs.mode===undefined?"Line":this.prefs.mode),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Filled" id="mode_Filled">Filled</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+i).attr("selected","selected");return a.append(l).append(m).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=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(c,a,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}if(b.show_counts!==undefined){this.prefs.show_counts=b.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;a.mode="Auto";if(a.mode_div){a.mode_div.remove()}this.ini t_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(d){a.mode_div=$("<div class='right-float menubutton popup' />").text("Display Mode");a.header_div.append(a.mode_div);a.mode="Auto";var c=function(e){a.mode_div.text(e);a.mode=e;a.tile_cache.clear();a.draw()};make_popupmenu(a.mode_div,{Auto:function(){c("Auto")},Dense:function(){c("Dense")},Squish:function(){c("Squish")},Pack:function(){c("Pack")}});a.data_cache.set(b,d);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z =[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,g,f,m,b,d,k,e,i){ n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>g){n.fillStyle=this.prefs.block_color;n.fillRect(k,i+1,e,9);n.fillStyle="#eee";for(var h=0,l=d.length;h<l;h++){if(b+h>=f&&b+h<=m){var a=Math.floor(Math.max(0,(b+h-f)*o));n.fillText(d[h],a+this.left_offset+j,i+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,i+4,e,3)}},draw_tile:function(X,h,n,al){var E=h*DENSITY*X,ad=(h+1)*DENSITY*X,D=DENSITY*X;var ae=E+"_"+ad;var z=this.data_cache.get(ae);if(z===undefined){this.data_queue[[E,ad]]=true;this.get_data(E,ad);return}var a=Math.ceil(D*al),L=$("<canvas class='tile'></canvas>"),Z=this.prefs.label_color,f=this.prefs.block_color,m=this.mode,V=(m==="Squish")||(m==="Dense")&&(m!=="Pack")||(m==="Auto"&&(z.extra_info==="no_detail")),P=this.left_offset,ak,s,am;if(z.dataset_type==="summary_tree"){s=30}else{if(m==="Dense"){s=15;am=10}else{am=(V?this.vertical_nodetail_px:this.vertical_detail_px);s=this.incremental_slots(this.view .zoom_res,z.data,V,m)*am+15;ak=this.inc_slots[this.view.zoom_res]}}L.css({position:"absolute",top:0,left:(E-this.view.low)*al-P});L.get(0).width=a+P;L.get(0).height=s;n.parent().css("height",Math.max(this.height_px,s)+"px");var A=L.get(0).getContext("2d"),ai=A.measureText("A").width;A.fillStyle=f;A.font=this.default_font;A.textAlign="right";if(z.dataset_type=="summary_tree"){var K,H=55,ac=255-H,g=ac*2/3,R=z.data,C=z.max,l=z.avg;if(R.length>2){var b=Math.ceil((R[1][0]-R[0][0])*al)}else{var b=50}for(var ag=0,w=R.length;ag<w;ag++){var T=Math.ceil((R[ag][0]-E)*al);var S=R[ag][1];if(!S){continue}K=Math.floor(ac-(S/C)*ac);A.fillStyle="rgb("+K+","+K+","+K+")";A.fillRect(T+P,0,b,20);if(this.prefs.show_counts){if(K>g){A.fillStyle="black"}else{A.fillStyle="#ddd"}A.textAlign="center";A.fillText(R[ag][1],T+P+(b/2),12)}}n.append(L);return L}var aj=z.data;var af=0;for(var ag=0,w=aj.length;ag<w;ag++){var M=aj[ag],J=M[0],ah=M[1],U=M[2],F=M[3];if(ah<=ad&&U>=E){var W=Math.floor(Math.max(0,(ah -E)*al)),B=Math.ceil(Math.min(a,Math.max(0,(U-E)*al))),Q=(m==="Dense"?0:ak[J]*am);if(z.dataset_type==="bai"){A.fillStyle=f;if(M[4] instanceof Array){var t=Math.floor(Math.max(0,(M[4][0]-E)*al)),I=Math.ceil(Math.min(a,Math.max(0,(M[4][1]-E)*al))),r=Math.floor(Math.max(0,(M[5][0]-E)*al)),p=Math.ceil(Math.min(a,Math.max(0,(M[5][1]-E)*al)));if(M[4][1]>=E&&M[4][0]<=ad){this.rect_or_text(A,al,ai,E,ad,M[4][0],M[4][2],t+P,I-t,Q)}if(M[5][1]>=E&&M[5][0]<=ad){this.rect_or_text(A,al,ai,E,ad,M[5][0],M[5][2],r+P,p-r,Q)}if(r>I){A.fillStyle="#999";A.fillRect(I+P,Q+5,r-I,1)}}else{A.fillStyle=f;this.rect_or_text(A,al,ai,E,ad,ah,F,W+P,B-W,Q)}if(m!=="Dense"&&!V&&ah>E){A.fillStyle=this.prefs.label_color;if(h===0&&W-A.measureText(F).width<0){A.textAlign="left";A.fillText(J,B+2+P,Q+8)}else{A.textAlign="right";A.fillText(J,W-2+P,Q+8)}A.fillStyle=f}}else{if(z.dataset_type==="interval_index"){if(V){A.fillRect(W+P,Q+5,B-W,1)}else{var v=M[4],O=M[5],Y=M[6],e=M[7];var u,aa,G=null,an=null;if(O&&Y){G=Math. floor(Math.max(0,(O-E)*al));an=Math.ceil(Math.min(a,Math.max(0,(Y-E)*al)))}if(m!=="Dense"&&F!==undefined&&ah>E){A.fillStyle=Z;if(h===0&&W-A.measureText(F).width<0){A.textAlign="left";A.fillText(F,B+2+P,Q+8)}else{A.textAlign="right";A.fillText(F,W-2+P,Q+8)}A.fillStyle=f}if(e){if(v){if(v=="+"){A.fillStyle=RIGHT_STRAND}else{if(v=="-"){A.fillStyle=LEFT_STRAND}}A.fillRect(W+P,Q,B-W,10);A.fillStyle=f}for(var ae=0,d=e.length;ae<d;ae++){var o=e[ae],c=Math.floor(Math.max(0,(o[0]-E)*al)),N=Math.ceil(Math.min(a,Math.max((o[1]-E)*al)));if(c>N){continue}u=5;aa=3;A.fillRect(c+P,Q+aa,N-c,u);if(G!==undefined&&!(c>an||N<G)){u=9;aa=1;var ab=Math.max(c,G),q=Math.min(N,an);A.fillRect(ab+P,Q+aa,q-ab,u)}}}else{u=9;aa=1;A.fillRect(W+P,Q+aa,B-W,u);if(M.strand){if(M.strand=="+"){A.fillStyle=RIGHT_STRAND_INV}else{if(M.strand=="-"){A.fillStyle=LEFT_STRAND_INV}}A.fillRect(W+P,Q,B-W,10);A.fillStyle=prefs.block_color}}}}}af++}}n.append(L);return L},gen_options:function(i){var a=$("<div />").addClass("for m-row");var e="track_"+i+"_block_color",k=$("<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(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;th is.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,b){FeatureTrack.call(this,c,a,b);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -1,7 +1,6 @@ /* Trackster 2010, James Taylor, Kanwei Li */ -var DEBUG = false; var DENSITY = 200, FEATURE_LEVELS = 10, @@ -37,15 +36,6 @@ left_img_inv.onload = function() { LEFT_STRAND_INV = CONTEXT.createPattern(left_img_inv, "repeat"); }; -function commatize( number ) { - number += ''; // Convert to string - var rgx = /(\d+)(\d{3})/; - while (rgx.test(number)) { - number = number.replace(rgx, '$1' + ',' + '$2'); - } - return number; -} - var Cache = function( num_elements ) { this.num_elements = num_elements; this.clear(); @@ -87,11 +77,11 @@ var View = function( chrom, title, vis_i this.label_tracks = []; this.max_low = 0; this.max_high = 0; - this.center = (this.max_high - this.max_low) / 2; + this.track_id_counter = 0; this.zoom_factor = 3; - this.zoom_level = 0; - this.track_id_counter = 0; + this.min_separation = 30; this.has_changes = false; + this.reset(); }; $.extend( View.prototype, { add_track: function ( track ) { @@ -129,27 +119,24 @@ var View = function( chrom, title, vis_i reset: function() { this.low = this.max_low; this.high = this.max_high; - this.center = this.center = (this.max_high - this.max_low) / 2; - this.zoom_level = 0; $(".yaxislabel").remove(); }, redraw: function(nodraw) { - this.span = this.max_high - this.max_low; - var span = this.span / Math.pow(this.zoom_factor, this.zoom_level), - low = this.center - (span / 2), - high = low + span; + var span = this.high - this.low, + low = this.low, + high = this.high; - if (low < 0) { - low = 0; - high = low + span; - - } else if (high > this.max_high) { + if (low < this.max_low) { + low = this.max_low; + } + if (high > this.max_high) { high = this.max_high; - low = high - span; + } + if (span < this.min_separation) { + high = low + this.min_separation; } this.low = Math.floor(low); this.high = Math.ceil(high); - this.center = Math.round( this.low + (this.high - this.low) / 2 ); // 10^log10(range / DENSITY) Close approximation for browser window, assuming DENSITY = window width this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / 200 ) / Math.LN10 ) ); @@ -157,9 +144,9 @@ var View = function( chrom, title, vis_i // Overview $("#overview-box").css( { - left: ( this.low / this.span ) * $("#overview-viewport").width(), + left: ( this.low / (this.max_high - this.max_low) ) * $("#overview-viewport").width(), // Minimum width for usability - width: Math.max( 12, ( ( this.high - this.low ) / this.span ) * $("#overview-viewport").width() ) + width: Math.max( 12, (this.high - this.low)/(this.max_high - this.max_low) * $("#overview-viewport").width() ) }).show(); $("#low").val( commatize(this.low) ); $("#high").val( commatize(this.high) ); @@ -174,26 +161,29 @@ var View = function( chrom, title, vis_i } } }, - zoom_in: function ( point, container ) { - if (this.max_high === 0 || this.high - this.low < 30) { + zoom_in: function (point, container) { + if (this.max_high === 0 || this.high - this.low < this.min_separation) { return; } - - if ( point ) { - this.center = point / container.width() * (this.high - this.low) + this.low; + var span = this.high - this.low, + cur_center = span / 2 + this.low, + new_half = (span / this.zoom_factor) / 2; + if (point) { + cur_center = point / container.width() * (this.high - this.low) + this.low; } - this.zoom_level += 1; + this.low = Math.round(cur_center - new_half); + this.high = Math.round(cur_center + new_half); this.redraw(); }, zoom_out: function () { if (this.max_high === 0) { return; } - if (this.zoom_level <= 0) { - this.zoom_level = 0; - return; - } - this.zoom_level -= 1; + var span = this.high - this.low, + cur_center = span / 2 + this.low, + new_half = (span * this.zoom_factor) / 2; + this.low = Math.round(cur_center - new_half); + this.high = Math.round(cur_center + new_half); this.redraw(); } }); @@ -269,8 +259,6 @@ var TiledTrack = function() { high = this.view.high, range = high - low, resolution = this.view.resolution; - - if (DEBUG) { $("#debug").text(resolution + " " + this.view.zoom_res); } var parent_element = $("<div style='position: relative;'></div>"), w_scale = this.content_div.width() / range, @@ -283,7 +271,7 @@ var TiledTrack = function() { var tile_index = Math.floor( low / resolution / DENSITY ); while ( ( tile_index * DENSITY * resolution ) < high ) { // Check in cache - var key = this.content_div.width() + '_' + this.view.zoom_level + '_' + tile_index; + var key = this.content_div.width() + '_' + w_scale + '_' + tile_index; var cached = this.tile_cache.get(key); if ( cached ) { // console.log("cached tile " + tile_index); --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -454,6 +454,15 @@ function init_history_items(historywrapp } } +function commatize( number ) { + number += ''; // Convert to string + var rgx = /(\d+)(\d{3})/; + while (rgx.test(number)) { + number = number.replace(rgx, '$1' + ',' + '$2'); + } + return number; +} + $(document).ready( function() { // Links with confirmation $( "a[confirm]" ).click( function() { --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -32,11 +32,11 @@ <div class="unified-panel-header" unselectable="on"><div class="unified-panel-header-inner">Trackster Visualization | ${config['title']} <a id="save-button" class="panel-header-button right-float" href="javascript:void(0);">Save</a> - <a id="refresh-button" class="panel-header-button right-float" href="javascript:void(0);">Refresh</a> + <a id="refresh-button" class="panel-header-button right-float" href="javascript:void(0);" onclick="view.update_options();return false;">Refresh</a></div></div><div id="content"> - <div id="top-labeltrack"></div> + <div id="top-labeltrack" style="position: relative;"></div><div id="viewport-container" style="overflow-x: hidden; overflow-y: auto;"><div id="viewport"></div></div> @@ -63,7 +63,6 @@ <img src="${h.url_for('/static/images/fugue/magnifier-zoom-out.png')}" /></a></form> - <div id="debug" style="float: right"></div></div></div></div> @@ -146,6 +145,9 @@ }); $("#content").bind("mousewheel", function( e, delta ) { + if (Math.abs(delta) < 0.5) { + return; + } if (delta > 0) { view.zoom_in(e.pageX, $("#viewport-container")); } else { @@ -166,19 +168,19 @@ this.current_x = e.offsetX; var delta_chrom = Math.round(delta / $(document).width() * view.span); - view.center += delta_chrom; + view.high += delta_chrom; + view.low += delta_chrom; view.redraw(); }); // To adjust the size of the viewport to fit the fixed-height footer var refresh = function( e ) { - $("#viewport-container").height( $(window).height() - 120 ); + $("#viewport-container").height( $(window).height() - 100 ); $("#nav-container").width( $("#center").width() ); view.redraw(); }; $(window).bind( "resize", function(e) { refresh(e); } ); - $("#right-border").bind( "click", function(e) { refresh(e); } ); - $("#right-border").bind( "dragend", function(e) { refresh(e); } ); + $("#right-border").bind( "click dragend", function(e) { refresh(e); } ); $(window).trigger( "resize" ); $("#viewport-container").bind( "dragstart", function( e ) { @@ -195,8 +197,9 @@ this.current_height = e.clientY; this.current_x = e.offsetX; - var delta_chrom = Math.round(delta / $(document).width() * (view.high - view.low)); - view.center -= delta_chrom; + var delta_chrom = Math.round(delta / $("#viewport-container").width() * (view.high - view.low)); + view.high -= delta_chrom; + view.low -= delta_chrom; view.redraw(); }); @@ -286,6 +289,35 @@ view.add_label_track( new LabelTrack( $("#top-labeltrack") ) ); view.add_label_track( new LabelTrack( $("#nav-labeltrack") ) ); + $("#top-labeltrack").bind( "dragstart", function(e) { + this.drag_origin_x = e.clientX; + this.drag_origin_pos = e.clientX / $("#viewport-container").width() * (view.high - view.low) + view.low; + this.drag_div = $("<div />").css( { + "height": $("#viewport-container").height(), "top": "0px", "position": "absolute", + "background-color": "#cfc", "border": "1px solid #6a6", "opacity": 0.5 + } ).appendTo( $(this) ); + }).bind( "drag", function(e) { + var min = Math.min(e.clientX, this.drag_origin_x), + max = Math.max(e.clientX, this.drag_origin_x), + span = (view.high - view.low), + width = $("#viewport-container").width(); + + $("#low").val(commatize(Math.round(min / width * span) + view.low)); + $("#high").val(commatize(Math.round(max / width * span) + view.low)); + this.drag_div.css( { "left": min + "px", "width": (max - min) + "px" } ); + }).bind( "dragend", function(e) { + var min = Math.min(e.clientX, this.drag_origin_x), + max = Math.max(e.clientX, this.drag_origin_x), + span = (view.high - view.low), + width = $("#viewport-container").width(), + old_low = view.low; + + view.low = Math.round(min / width * span) + old_low; + view.high = Math.round(max / width * span) + old_low; + this.drag_div.remove(); + view.redraw(); + }); + $.ajax({ url: "${h.url_for( action='chroms' )}", %if config.get('vis_id'): --- a/static/trackster.css +++ b/static/trackster.css @@ -111,7 +111,6 @@ .label-track { /* font-weight: bold; */ /* font-size: 10px; */ - } .label-track .label { border-left: solid #999 1px;

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galaxy-dist commit e4d2a5c24b05: Minor fix for changing datatype test.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg <dan(a)bx.psu.edu> # Date 1275586314 14400 # Node ID e4d2a5c24b05e164dc37918574d7078f07fc6b67 # Parent 6d218af7906af1f9524d02f785885bf1fd508f16 Minor fix for changing datatype test. --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -626,7 +626,7 @@ class TwillTestCase( unittest.TestCase ) self.check_page_for_string( 'This will change the datatype of the existing dataset but' ) tc.fv( 'change_datatype', 'datatype', datatype ) tc.submit( 'change' ) - self.check_page_for_string( 'Edit Attributes' ) + self.check_page_for_string( 'Changed the type of dataset' ) self.home() def copy_history_item( self, source_dataset_ids='', target_history_ids=[], all_target_history_ids=[], deleted_history_ids=[] ): @@ -2080,4 +2080,3 @@ class TwillTestCase( unittest.TestCase ) def add_tag( self, item_id, item_class, context, new_tag, check_str='' ): self.visit_url( "%s/tag/add_tag_async?item_id=%s&item_class=%s&context=%s&new_tag=%s" % \ ( self.url, item_id, item_class, context, new_tag ) ) -

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galaxy-dist commit d25af565d085: Bug fix for importing a history archive.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '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 1275599071 14400 # Node ID d25af565d085e19dccb8f20c857e633397e5da08 # Parent 170e2688d37043c9f1c4349f15d29ce6dd43e88b Bug fix for importing a history archive. --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -454,7 +454,7 @@ class HistoryController( BaseController, # Security check: make sure that members are relative, not absolute. for tarinfo in history_archive_file.getmembers(): - if tarinfo.name.startswith("/") or tarinfo.name.startswith(".."): + if tarinfo.name.startswith("/") or tarinfo.name.find("..") != -1: return trans.show_error_message( 'Error importing history archive: archive file is invalid.' ) # Unpack archive in temporary directory.

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galaxy-dist commit 170e2688d370: Improvements to history import/export archive: (a) use python tar file support (which may be more widely available than pax) and (b) perform some simple security checks to ensure that uploaded archive files are not malicious.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '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 1275595159 14400 # Node ID 170e2688d37043c9f1c4349f15d29ce6dd43e88b # Parent e4d2a5c24b05e164dc37918574d7078f07fc6b67 Improvements to history import/export archive: (a) use python tar file support (which may be more widely available than pax) and (b) perform some simple security checks to ensure that uploaded archive files are not malicious. --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -9,7 +9,7 @@ from galaxy.util.sanitize_html import sa from galaxy.tools.actions import upload_common from galaxy.tags.tag_handler import GalaxyTagHandler from sqlalchemy.sql.expression import ClauseElement -import webhelpers, logging, operator, tempfile, subprocess, shutil +import webhelpers, logging, operator, tempfile, subprocess, shutil, tarfile from datetime import datetime from cgi import escape @@ -449,17 +449,18 @@ class HistoryController( BaseController, if archived_history is not None: # Import archived history. - try: - archive_file = archived_history.file - + try: + history_archive_file = tarfile.open( archived_history.file.name ) + + # Security check: make sure that members are relative, not absolute. + for tarinfo in history_archive_file.getmembers(): + if tarinfo.name.startswith("/") or tarinfo.name.startswith(".."): + return trans.show_error_message( 'Error importing history archive: archive file is invalid.' ) + # Unpack archive in temporary directory. temp_output_dir = tempfile.mkdtemp() - cmd = "pax -z -r < %s " % archive_file.name - temp_stderr_name = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name - temp_stderr = open( temp_stderr_name, 'wb' ) - proc = subprocess.Popen( args=cmd, shell=True, cwd=temp_output_dir, stderr=temp_stderr.fileno() ) - returncode = proc.wait() - temp_stderr.close() + history_archive_file.extractall( path=temp_output_dir ) + history_archive_file.close() # Read history attributes. history_attr_in = open( '%s/%s' % ( temp_output_dir, 'history_attrs.txt'), 'rb' ) @@ -625,24 +626,14 @@ class HistoryController( BaseController, os.rename( datasets_attrs_file_name, new_name ) datasets_attrs_file_name = new_name - # Write temp file with all files to archive. These files are (a) history attributes file; (b) datasets attributes file; and (c) - # datasets files. - archive_list_file_name = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name - archive_list_out = open( archive_list_file_name, 'w' ) - archive_list_out.write( '%s\n' % history_attrs_file_name ) - archive_list_out.write( '%s\n' % datasets_attrs_file_name ) - for dataset in datasets: - archive_list_out.write( '%s\n' % dataset.file_name ) - archive_list_out.close() - - # Use 'pax' to create compressed tar archive of history's datasets. -s options uses a regular expression to replace path - # information. - cmd = "pax -w -s ',.*history_attrs.txt,history_attrs.txt,' -s ',.*datasets_attrs.txt,datasets_attrs.txt,' -s ',/.*/,datasets/,' -x tar -z -f %s.tar.gz < %s" % ( trans.security.encode_id( history.id ), archive_list_file_name ) - temp_stderr_name = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name - temp_stderr = open( temp_stderr_name, 'wb' ) - proc = subprocess.Popen( args=cmd, shell=True, cwd=history_export_dir_name, stderr=temp_stderr.fileno() ) - returncode = proc.wait() - temp_stderr.close() + # Write files to archive: (a) history attributes file; (b) datasets attributes file; and (c) datasets files. + history_archive_name = '%s/%s.tar.gz' % ( history_export_dir_name, trans.security.encode_id( history.id ) ) + history_archive = tarfile.open( history_archive_name, "w:gz" ) + history_archive.add( history_attrs_file_name, arcname="history_attrs.txt" ) + history_archive.add( datasets_attrs_file_name, arcname="datasets_attrs.txt" ) + for i, dataset in enumerate( datasets ) : + history_archive.add( dataset.file_name, arcname="datasets/%s" % datasets_attrs[i]['file_name'] ) + history_archive.close() # Remove temp directory. if os.path.exists( temp_output_dir ): @@ -652,14 +643,13 @@ class HistoryController( BaseController, return trans.show_error_message( 'Error creating history archive. ' + str( e ) ) # Stream archive. - archive_file_name = '%s/%s.tar.gz' % ( history_export_dir_name, trans.security.encode_id( history.id ) ) - if os.path.exists( archive_file_name ): + if os.path.exists( history_archive_name ): valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' hname = history.name hname = ''.join(c in valid_chars and c or '_' for c in hname)[0:150] trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy-History-%s.tar.gz" % ( hname ) trans.response.set_content_type( 'application/x-gzip' ) - return open( archive_file_name ) + return open( history_archive_name ) else: return

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galaxy-dist commit a12eeed213ff: Resync Annotation Profiler tests to current cached data.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg <dan(a)bx.psu.edu> # Date 1275511239 14400 # Node ID a12eeed213ff6d8581073ad77914b12dfc26f9bd # Parent 1dba26a363abfb488b8021f3c86c75651fce81b0 Resync Annotation Profiler tests to current cached data. --- a/test-data/annotation_profiler_1.out +++ b/test-data/annotation_profiler_1.out @@ -1,8 +1,8 @@ chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + multiz17way 1700000 1 -chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + knownAlt 14617 57 +chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + mrna 1476531 12 chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + multiz28way 1700000 1 chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + refGene 1247808 15 -chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + mrna 1476531 12 +chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + knownAlt 14617 57 chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + affyGnf1h 16218 2 chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + snp126 8224 7262 chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + acembly 1532618 20 --- a/tools/annotation_profiler/annotation_profiler.xml +++ b/tools/annotation_profiler/annotation_profiler.xml @@ -27,14 +27,14 @@ <param name="input1" value="4.bed" dbkey="hg18"/><param name="keep_empty" value=""/><param name="summary" value=""/> - <param name="table_names" value="acembly,affyGnf1h,affyHuEx1,knownAlt,knownGene,mrna,multiz17way,multiz28way,refGene,snp126"/> + <param name="table_names" value="acembly,affyGnf1h,knownAlt,knownGene,mrna,multiz17way,multiz28way,refGene,snp126"/><output name="out_file1" file="annotation_profiler_1.out" /></test><test><param name="input1" value="3.bed" dbkey="hg18"/><param name="keep_empty" value=""/><param name="summary" value="Summary"/> - <param name="table_names" value="acembly,affyGnf1h,affyHuEx1,knownAlt,knownGene,mrna,multiz17way,multiz28way,refGene,snp126"/> + <param name="table_names" value="acembly,affyGnf1h,knownAlt,knownGene,mrna,multiz17way,multiz28way,refGene,snp126"/><output name="out_file1" file="annotation_profiler_2.out" /></test></tests> --- a/test-data/annotation_profiler_2.out +++ b/test-data/annotation_profiler_2.out @@ -1,9 +1,9 @@ #tableName tableChromosomeCoverage tableChromosomeCount tableRegionCoverage tableRegionCount allIntervalCount allIntervalSize allCoverage allTableRegionsOverlaped allIntervalsOverlapingTable nrIntervalCount nrIntervalSize nrCoverage nrTableRegionsOverlaped nrIntervalsOverlapingTable multiz17way 1232617592 115 107496500 7 25 2178864 2178864 25 25 24 2178828 2178828 7 24 -knownAlt 8647368 20213 766619 1630 25 2178864 5612 31 11 24 2178828 5612 31 11 +mrna 610115393 8453 53577685 617 25 2178864 1904380 38 24 24 2178828 1904344 33 23 multiz28way 1233785185 143 107466479 10 25 2178864 2178864 25 25 24 2178828 2178828 8 24 refGene 496767116 7324 46112187 488 25 2178864 1677947 30 23 24 2178828 1677911 27 22 -mrna 610115393 8453 53577685 617 25 2178864 1904380 38 24 24 2178828 1904344 33 23 +knownAlt 8647368 20213 766619 1630 25 2178864 5612 31 11 24 2178828 5612 31 11 affyGnf1h 24034558 3995 2446754 307 25 2178864 191851 9 6 24 2178828 191851 9 6 snp126 5297125 4456213 382226 331523 25 2178864 9205 7074 25 24 2178828 9205 7074 24 acembly 710938193 13800 63146381 938 25 2178864 1903560 35 24 24 2178828 1903524 30 23

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