2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b7e8d3695852/ changeset: b7e8d3695852 user: james_taylor date: 2013-02-04 05:12:58 summary: templates: Move external_services templates into templates/webapps/galaxy affected #: 6 files diff -r 35e476a0c0c4a453396010629030c77575fbec95 -r b7e8d36958522a031a937dc50034b3a57fefe3ed templates/external_services/generic_jquery_grid.mako --- a/templates/external_services/generic_jquery_grid.mako +++ /dev/null @@ -1,59 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="json_common.mako" import="display_item" /> - -<%def name="title()">${param_dict['service_instance'].name}: ${action.label}</%def> - -<%def name="display_json_grid_result( headers, rows )"> - %for row in rows: - %for name in headers: - <div class="form-row"> - <label>${name}</label> - ${display_item( row.get( name ) )} - <div style="clear: both"></div> - </div> - %endfor - %endfor -</%def> - -<% - #HACK!!!! need to use better method of displaying jqGrid here, needs to allow paging as optionally available. - if 'Rows' in result: #paged - records = result['Records'] - total = result['Total'] - rows = result['Rows'] - page = result['Page'] - else: - rows = result - records = None - total = None - page = None - headers = rows[0].keys() -%> - -<div class="toolForm"> - <div class="toolFormTitle">${action.label} of ${param_dict['service_instance'].name} (${param_dict['service'].name}) on ${param_dict['item'].name}</div> - <div class="toolFormBody"> - %if records: - <div class="form-row"> - <label>Records</label> - ${records} - <div style="clear: both"></div> - </div> - %endif - %if total: - <div class="form-row"> - <label>Total</label> - ${total} - <div style="clear: both"></div> - </div> - %endif - %if page: - <div class="form-row"> - <label>Page</label> - ${page} - <div style="clear: both"></div> - </div> - %endif - ${display_json_grid_result( headers, rows )} - </div> -</div> diff -r 35e476a0c0c4a453396010629030c77575fbec95 -r b7e8d36958522a031a937dc50034b3a57fefe3ed templates/external_services/generic_json.mako --- a/templates/external_services/generic_json.mako +++ /dev/null @@ -1,11 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="json_common.mako" import="display_item" /> - -<%def name="title()">${action.label} of ${param_dict['service_instance'].name} (${param_dict['service'].name}) on ${param_dict['item'].name}</%def> - -<div class="toolForm"> - <div class="toolFormTitle">${action.label} of ${param_dict['service_instance'].name} (${param_dict['service'].name}) on ${param_dict['item'].name}</i></div> - <div class="toolFormBody"> - ${display_item( result )} - </div> -</div> diff -r 35e476a0c0c4a453396010629030c77575fbec95 -r b7e8d36958522a031a937dc50034b3a57fefe3ed templates/external_services/json_common.mako --- a/templates/external_services/json_common.mako +++ /dev/null @@ -1,28 +0,0 @@ - -<%def name="display_dict( result_dict )"> - %for key, value in result_dict.items(): - <div class="form-row"> - <label>${key}</label> - ${display_item( value )} - <div style="clear: both"></div> - </div> - %endfor -</%def> - -<%def name="display_list( items )"> - <ul> - %for item in items: - <li>${display_item( item ) }</li> - %endfor - </ul> -</%def> - -<%def name="display_item( item )"> - %if isinstance( item, ( list, tuple ) ): - ${display_list( item )} - %elif isinstance( item, dict ): - ${display_dict( item )} - %else: - ${item} - %endif -</%def> diff -r 35e476a0c0c4a453396010629030c77575fbec95 -r b7e8d36958522a031a937dc50034b3a57fefe3ed templates/webapps/galaxy/external_services/generic_jquery_grid.mako --- /dev/null +++ b/templates/webapps/galaxy/external_services/generic_jquery_grid.mako @@ -0,0 +1,59 @@ +<%inherit file="/base.mako"/> +<%namespace file="json_common.mako" import="display_item" /> + +<%def name="title()">${param_dict['service_instance'].name}: ${action.label}</%def> + +<%def name="display_json_grid_result( headers, rows )"> + %for row in rows: + %for name in headers: + <div class="form-row"> + <label>${name}</label> + ${display_item( row.get( name ) )} + <div style="clear: both"></div> + </div> + %endfor + %endfor +</%def> + +<% + #HACK!!!! need to use better method of displaying jqGrid here, needs to allow paging as optionally available. + if 'Rows' in result: #paged + records = result['Records'] + total = result['Total'] + rows = result['Rows'] + page = result['Page'] + else: + rows = result + records = None + total = None + page = None + headers = rows[0].keys() +%> + +<div class="toolForm"> + <div class="toolFormTitle">${action.label} of ${param_dict['service_instance'].name} (${param_dict['service'].name}) on ${param_dict['item'].name}</div> + <div class="toolFormBody"> + %if records: + <div class="form-row"> + <label>Records</label> + ${records} + <div style="clear: both"></div> + </div> + %endif + %if total: + <div class="form-row"> + <label>Total</label> + ${total} + <div style="clear: both"></div> + </div> + %endif + %if page: + <div class="form-row"> + <label>Page</label> + ${page} + <div style="clear: both"></div> + </div> + %endif + ${display_json_grid_result( headers, rows )} + </div> +</div> diff -r 35e476a0c0c4a453396010629030c77575fbec95 -r b7e8d36958522a031a937dc50034b3a57fefe3ed templates/webapps/galaxy/external_services/generic_json.mako --- /dev/null +++ b/templates/webapps/galaxy/external_services/generic_json.mako @@ -0,0 +1,11 @@ +<%inherit file="/base.mako"/> +<%namespace file="json_common.mako" import="display_item" /> + +<%def name="title()">${action.label} of ${param_dict['service_instance'].name} (${param_dict['service'].name}) on ${param_dict['item'].name}</%def> + +<div class="toolForm"> + <div class="toolFormTitle">${action.label} of ${param_dict['service_instance'].name} (${param_dict['service'].name}) on ${param_dict['item'].name}</i></div> + <div class="toolFormBody"> + ${display_item( result )} + </div> +</div> diff -r 35e476a0c0c4a453396010629030c77575fbec95 -r b7e8d36958522a031a937dc50034b3a57fefe3ed templates/webapps/galaxy/external_services/json_common.mako --- /dev/null +++ b/templates/webapps/galaxy/external_services/json_common.mako @@ -0,0 +1,28 @@ + +<%def name="display_dict( result_dict )"> + %for key, value in result_dict.items(): + <div class="form-row"> + <label>${key}</label> + ${display_item( value )} + <div style="clear: both"></div> + </div> + %endfor +</%def> + +<%def name="display_list( items )"> + <ul> + %for item in items: + <li>${display_item( item ) }</li> + %endfor + </ul> +</%def> + +<%def name="display_item( item )"> + %if isinstance( item, ( list, tuple ) ): + ${display_list( item )} + %elif isinstance( item, dict ): + ${display_dict( item )} + %else: + ${item} + %endif +</%def> https://bitbucket.org/galaxy/galaxy-central/commits/17c40da527fe/ changeset: 17c40da527fe user: james_taylor date: 2013-02-04 05:21:17 summary: genetrack: Purge all genetrack support (since it no longer exists), other than leaving filetype for backward compatibility affected #: 13 files diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -26,7 +26,6 @@ <converter file="bed_to_summary_tree_converter.xml" target_datatype="summary_tree"/><converter file="bed_to_fli_converter.xml" target_datatype="fli"/><!-- <display file="ucsc/interval_as_bed.xml" /> --> - <display file="genetrack.xml" /><display file="igb/bed.xml" /></datatype><datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true"> @@ -34,7 +33,6 @@ </datatype><datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" /><datatype extension="bed6" type="galaxy.datatypes.interval:Bed6"> - <converter file="bed_to_genetrack_converter.xml" target_datatype="genetrack"/></datatype><datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" /><datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true"> diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 display_applications/genetrack.xml --- a/display_applications/genetrack.xml +++ /dev/null @@ -1,18 +0,0 @@ -<display id="genetrack_interval" version="1.0.0" name="view in"> - <link id="genetrack" name="GeneTrack"> - <url target_frame="galaxy_main">http://genetrack.g2.bx.psu.edu/galaxy?filename=${encoded_filename.qp}&hashkey=${hash_key.qp}&input=${qp(str($genetrack_file.id))}&GALAXY_URL=${galaxy_url.qp}</url> - <param type="data" name="bed_file" viewable="False" format="bed6,genetrack"/><!-- for now, we'll explicitly take care of the multi-step conversion; walk genetrack datatype down as a conversion of genetrack to genetrack doesn't exist and would likely be pointless --> - <param type="data" dataset="bed_file" name="genetrack_file" format="genetrack" viewable="False" /> - <param type="template" name="galaxy_url" strip="True" > - ${BASE_URL}/tool_runner?tool_id=predict2genetrack - </param> - <param type="template" name="hash_key" strip="True" > - #from galaxy.util.hash_util import hmac_new - ${hmac_new( $APP.config.tool_secret, $genetrack_file.file_name )} - </param> - <param type="template" name="encoded_filename" strip="True" > - #import binascii - ${binascii.hexlify( $genetrack_file.file_name )} - </param> - </link> -</display> diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -143,7 +143,6 @@ self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) ) self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",") - self.genetrack_display_sites = kwargs.get( 'genetrack_display_sites', "main,test" ).lower().split(",") self.brand = kwargs.get( 'brand', None ) self.support_url = kwargs.get( 'support_url', 'http://wiki.g2.bx.psu.edu/Support' ) self.wiki_url = kwargs.get( 'wiki_url', 'http://g2.trac.bx.psu.edu/' ) diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 lib/galaxy/datatypes/converters/bed_to_genetrack_converter.py --- a/lib/galaxy/datatypes/converters/bed_to_genetrack_converter.py +++ /dev/null @@ -1,44 +0,0 @@ -#!/usr/bin/env python - -#FIXME: THIS IS 1:1 COPY OF THE SAME FUNCTIONED TOOL - ALLOW REGULAR TOOLS TO MASCARADE AS CONVERTERS - -""" -Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy. - -usage: %prog input output shift -""" - -import sys, shutil, os -from galaxy import eggs -import pkg_resources -pkg_resources.require( "GeneTrack" ) - -from genetrack.scripts import tabs2genetrack -from genetrack import logger - -if __name__ == "__main__": - import os - os.environ[ 'LC_ALL' ] = 'C' - #os.system( 'export' ) - - parser = tabs2genetrack.option_parser() - - options, args = parser.parse_args() - - # uppercase the format - options.format = options.format.upper() - - if options.format not in ('BED', 'GFF'): - sys.stdout = sys.stderr - parser.print_help() - sys.exit(-1) - - logger.disable(options.verbosity) - - # missing file names - if not (options.inpname and options.outname and options.format): - parser.print_help() - sys.exit(-1) - else: - tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\ - format=options.format, shift=options.shift, index=options.index, options=options) diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 lib/galaxy/datatypes/converters/bed_to_genetrack_converter.xml --- a/lib/galaxy/datatypes/converters/bed_to_genetrack_converter.xml +++ /dev/null @@ -1,17 +0,0 @@ -<tool id="CONVERTER_bed_to_genetrack_0" name="Convert BED to GeneTrack Index" version="1.0.1"> -<!-- FIXME: THIS IS ALMOST 1:1 COPY OF THE SAME FUNCTIONED TOOL - ALLOW REGULAR TOOLS TO MASCARADE AS CONVERTERS -Using a shift of 0, but tool allows specifying... ---> -<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --> - <command interpreter="python">bed_to_genetrack_converter.py -i $input1 -o $output1 -s 0 -v 0 -f BED -x</command> - <inputs> - <page> - <param format="bed6" name="input1" type="data" label="Choose BED file"/> - </page> - </inputs> - <outputs> - <data format="genetrack" name="output1"/> - </outputs> - <help> - </help> -</tool> diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 lib/galaxy/datatypes/tracks.py --- a/lib/galaxy/datatypes/tracks.py +++ b/lib/galaxy/datatypes/tracks.py @@ -10,27 +10,30 @@ log = logging.getLogger(__name__) +# GeneTrack is no longer supported but leaving the datatype since +# files of this type may still exist + class GeneTrack( binary.Binary ): file_ext = "genetrack" def __init__(self, **kwargs): super( GeneTrack, self ).__init__( **kwargs ) - self.add_display_app( 'genetrack', 'View in', '', 'genetrack_link' ) - def get_display_links( self, dataset, type, app, base_url, target_frame='galaxy_main', **kwd ): #Force target_frame to be 'galaxy_main' - return binary.Binary.get_display_links( self, dataset, type, app, base_url, target_frame=target_frame, **kwd ) - def genetrack_link( self, hda, type, app, base_url ): - ret_val = [] - if hda.dataset.has_data(): - # Get the disk file name and data id - file_name = hda.dataset.get_file_name() - data_id = quote_plus( str( hda.id ) ) - galaxy_url = quote_plus( "%s%s" % ( base_url, url_for( controller = 'tool_runner', tool_id='predict2genetrack' ) ) ) - # Make it secure - hashkey = quote_plus( hmac_new( app.config.tool_secret, file_name ) ) - encoded = quote_plus( binascii.hexlify( file_name ) ) - for name, url in util.get_genetrack_sites(): - if name.lower() in app.config.genetrack_display_sites: - # send both parameters filename and hashkey - link = "%s?filename=%s&hashkey=%s&input=%s&GALAXY_URL=%s" % ( url, encoded, hashkey, data_id, galaxy_url ) - ret_val.append( ( name, link ) ) - return ret_val + # self.add_display_app( 'genetrack', 'View in', '', 'genetrack_link' ) + # def get_display_links( self, dataset, type, app, base_url, target_frame='galaxy_main', **kwd ): #Force target_frame to be 'galaxy_main' + # return binary.Binary.get_display_links( self, dataset, type, app, base_url, target_frame=target_frame, **kwd ) + # def genetrack_link( self, hda, type, app, base_url ): + # ret_val = [] + # if hda.dataset.has_data(): + # # Get the disk file name and data id + # file_name = hda.dataset.get_file_name() + # data_id = quote_plus( str( hda.id ) ) + # galaxy_url = quote_plus( "%s%s" % ( base_url, url_for( controller = 'tool_runner', tool_id='predict2genetrack' ) ) ) + # # Make it secure + # hashkey = quote_plus( hmac_new( app.config.tool_secret, file_name ) ) + # encoded = quote_plus( binascii.hexlify( file_name ) ) + # for name, url in util.get_genetrack_sites(): + # if name.lower() in app.config.genetrack_display_sites: + # # send both parameters filename and hashkey + # link = "%s?filename=%s&hashkey=%s&input=%s&GALAXY_URL=%s" % ( url, encoded, hashkey, data_id, galaxy_url ) + # ret_val.append( ( name, link ) ) + # return ret_val diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py +++ b/lib/galaxy/eggs/__init__.py @@ -349,7 +349,7 @@ raise EggNotFetchable( missing ) class GalaxyConfig( object ): - always_conditional = ( 'GeneTrack', 'pysam', 'ctypes', 'python_daemon' ) + always_conditional = ( 'pysam', 'ctypes', 'python_daemon' ) def __init__( self, config_file ): if config_file is None: self.config = None @@ -387,7 +387,6 @@ "guppy": lambda: self.config.get( "app:main", "use_memdump" ), "python_openid": lambda: self.config.get( "app:main", "enable_openid" ), "python_daemon": lambda: sys.version_info[:2] >= ( 2, 5 ), - "GeneTrack": lambda: sys.version_info[:2] >= ( 2, 5 ), "ctypes": lambda: ( "drmaa" in self.config.get( "app:main", "start_job_runners" ).split(",") ) and sys.version_info[:2] == ( 2, 4 ), "pysam": lambda: check_pysam() }.get( egg_name, lambda: True )() diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -432,11 +432,6 @@ if build in site['builds']: sites.append((site['name'],site['url'])) return sites -def get_genetrack_sites(): - sites = [] - for site in genetrack_sites: - sites.append( ( site['name'], site['url'] ) ) - return sites def read_dbnames(filename): """ Read build names from file """ @@ -773,7 +768,6 @@ ncbi_names = read_ncbi( os.path.join( galaxy_root_path, "tool-data", "shared", "ncbi", "builds.txt" ) ) ucsc_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "ucsc_build_sites.txt" ) ) gbrowse_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "gbrowse", "gbrowse_build_sites.txt" ) ) -genetrack_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "genetrack", "genetrack_sites.txt" ), check_builds=False ) dlnames = dict(ucsc=ucsc_names, ensembl=ensembl_names, ncbi=ncbi_names) def galaxy_directory(): diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 templates/genetrack/base.html --- a/templates/genetrack/base.html +++ /dev/null @@ -1,29 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml"> -<head> -<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> -<title>${self.title()}</title> -<link rel="stylesheet" href="${h.url_for('/static/genetrack/genetrack.css')}" type="text/css" media="screen"> -<script type="text/javascript" src="${h.url_for('/static/genetrack/genetrack.js')}">var dummy1=0;</script> -</head> - -<%def name="title()"> - Title -</%def> - -<%def name="footer()"> - <div align="center" id="footer"> - <a href="/">Home</a> | <a href="${h.url_for(controller='genetrack',action='search',dataset_id=dataset_id)}">Search</a> - </div> - <div align="center" id="tag"> - Powered by <a href="http://genetrack.googlecode.com">GeneTrack</a> | - <a href="http://atlas.bx.psu.edu/">Penn State Genome Cartography (2008)</a> - </div> -</%def> - -<body> - ${self.body()} - ${self.footer()} -</body> - -</html> diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 templates/genetrack/index.html --- a/templates/genetrack/index.html +++ /dev/null @@ -1,75 +0,0 @@ -## index.html -<%inherit file="base.html"/> -<%def name="title()"> - Index -</%def> - -<h1 align="center">${conf.TITLE}</h1> - -<form action="" method="get"> - -<table align="center" cellpadding="2" cellspacing="1" width="100%"> - - - % if form.errors(): - <tr class="error"><td align="center"> - % for ekey, evalue in form.errors().items(): - <b>ERROR:</b> ${ekey}: ${evalue}<br> - % endfor - </td></tr> - % endif - - <tr class="grey"> - <td colspan="4" align="center"> - <a href="javascript:toggle('options')">More</a><img src="/static/images/thumbtack_icon.png" align="absmiddle" border="0"> - - Chromosome: ${form.chrom.tag()} - Feature: ${form.feature.tag()} - Width: ${form.zoom.tag()} - Plot: ${form.plot.tag()} - <input type="submit" name="submit" value="Display!"> - <div id="options" style="display:none" class="selected"> - <table cellpadding="3"> - <tr> - <td> - <!-- Nucleosome:${form.nuc_track.tag()} - ORF:${form.orf_track.tag()} - --> - Fit threshold: ${form.min_fit.tag()} - Image width: ${form.img_size.tag()} - </td> - </tr> - </table> - </div> - - </td> - </tr> - - <tr> - <td align="center"> - <input type="submit" name="move_left" value="<< Move Left"> - - <input type="submit" name="zoom_out" value="Shrink -"> - - <input type="submit" name="zoom_in" value="Magnify +"> - - <input type="submit" name="move_right" value="Move Right >>"> - </td> - </tr> - - <tr> - <td align="center"> - <img src="${h.url_for('/static/genetrack/plots/' + param.fname)}" align="center" border="0"> - </td> - </tr> - - <tr> - <td align="center"> - <!-- <a href='/search'>Search</a> --> - </td> - </tr> - -</table> - -<input type="hidden" id="dataset_id" name="dataset_id" value="${dataset_id}" /> -</form> diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 templates/genetrack/invalid.html --- a/templates/genetrack/invalid.html +++ /dev/null @@ -1,3 +0,0 @@ -## index.html -<%inherit file="base.html"/> -<h1>This dataset is not a valid GeneTrack dataset.</h1> diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 templates/genetrack/search.html --- a/templates/genetrack/search.html +++ /dev/null @@ -1,55 +0,0 @@ -## search.html -<%! -from itertools import cycle -colors = cycle( [ 'even', 'odd' ] ) -%> - -<%inherit file="base.html"/> -<%def name="title()"> - Search -</%def> - -<h1 align="center">Search</h1> - -<div align="center"> - <form action="search" method="get"> - Search terms <input type="text" name="word" value="${param.word}"> - <input type="hidden" name="dataset_id" id="dataset_id" value="${dataset_id}" /> - <input type="submit" name="submit" value="Search!"> - </form> -</div> - -% if param.word: - - % if len(query)>0: - <h4 align="center">Showing the best ${len(query)} matches</h4> - - <table align="center" class="data_table" cellpadding="6" cellspacing="0"> - <tr align="center"> - <th width="25%">Name</td> - <th width="25%">Chromosome</td> - <th width="25%">Start:End</td> - <th width="25%">Type</td> - </tr> - % for color, row in zip(colors, query): - ${makerow(color, row)} - % endfor - </table> - - % else: - <h4 align="center">No results found</h4> - % endif - -%endif - -<br> -<%def name="makerow(color, row)"> - <tr class="${color}" align="center"> - <td><a href="${h.url_for(controller='genetrack', action='index', chrom=row.chrom, feature=row.start, dataset_id=dataset_id)}">${row.name}</a></td> - <td>${row.chrom}</td> - <td>${row.start}:${row.end}</td> - <td>${row.label.name}</td> - </tr> -</%def> - -</form> diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 tool-data/shared/genetrack/genetrack_sites.txt --- a/tool-data/shared/genetrack/genetrack_sites.txt +++ /dev/null @@ -1,7 +0,0 @@ -# GeneTrack sites -# -# The key(s) should be added to universe_wsgi.ini as the value of -# genetrack_display_sites -# -# key site url -psu_galaxy http://genetrack.g2.bx.psu.edu/galaxy Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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