February 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: james_taylor: remove comment from sentry middleware that is not a valid doctest
by Bitbucket 03 Feb '13

03 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/898c9e140da9/ changeset: 898c9e140da9 user: james_taylor date: 2013-02-04 05:27:04 summary: remove comment from sentry middleware that is not a valid doctest affected #: 1 file diff -r b59a3df615c3542cb05ad68dc851669928a586d8 -r 898c9e140da953fe18ebfda5a96b9810d372706d lib/galaxy/web/framework/middleware/sentry.py --- a/lib/galaxy/web/framework/middleware/sentry.py +++ b/lib/galaxy/web/framework/middleware/sentry.py @@ -16,9 +16,6 @@ """ A WSGI middleware which will attempt to capture any uncaught exceptions and send them to Sentry. - - >>> from raven.base import Client - >>> application = Sentry(application, Client()) """ def __init__(self, application, dsn): self.application = application Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: james_taylor: Add some missing files
by Bitbucket 03 Feb '13

03 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b59a3df615c3/ changeset: b59a3df615c3 user: james_taylor date: 2013-02-04 05:22:16 summary: Add some missing files affected #: 2 files diff -r 17c40da527fe8fee481ead85bdf8069776fc8f44 -r b59a3df615c3542cb05ad68dc851669928a586d8 lib/galaxy/web/framework/middleware/request_id.py --- /dev/null +++ b/lib/galaxy/web/framework/middleware/request_id.py @@ -0,0 +1,12 @@ +import uuid + +class RequestIDMiddleware( object ): + """ + A WSGI middleware that creates a unique ID for the request and + puts it in the environment + """ + def __init__( self, app, global_conf=None ): + self.app = app + def __call__( self, environ, start_response ): + environ['request_id'] = uuid.uuid1().hex + return self.app( environ, start_response ) \ No newline at end of file diff -r 17c40da527fe8fee481ead85bdf8069776fc8f44 -r b59a3df615c3542cb05ad68dc851669928a586d8 static/scripts/packed/libs/jquery/select2.js --- /dev/null +++ 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C=this.parent.prepareOpts.apply(this,arguments);if(C.element.get(0).tagName.toLowerCase()==="select"){C.initSelection=function(D,F){var E=[];D.find(":selected").each2(function(G,H){E.push({id:H.attr("value"),text:H.text()})});if(j.isFunction(F)){F(E)}}}return C},initContainer:function(){var C=".select2-choices",D;this.searchContainer=this.container.find(".select2-search-field");this.selection=D=this.container.find(C);this.search.bind("keydown",this.bind(function(F){if(!this.enabled){return}if(F.which===c.BACKSPACE&&this.search.val()===""){this.close();var G,E=D.find(".select2-search-choice-focus");if(E.length>0){this.unselect(E.first());this.search.width(10);d(F);return}G=D.find(".select2-search-choice");if(G.length>0){G.last().addClass("select2-search-choice-focus")}}else{D.find(".select2-search-choice-focus").removeClass("select2-search-choice-focus")}if(this.opened()){switch(F.which){case c.UP:case c.DOWN:this.moveHighlight((F.which===c.UP)?-1:1);d(F);return;case c.ENTER:case 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c.ESC:this.cancel(F);d(F);return}}if(F.which===c.TAB||c.isControl(F)||c.isFunctionKey(F)||F.which===c.BACKSPACE||F.which===c.ESC){return}if(this.opts.openOnEnter===false&&F.which===c.ENTER){return}this.open();if(F.which===c.PAGE_UP||F.which===c.PAGE_DOWN){d(F)}}));this.search.bind("keyup",this.bind(this.resizeSearch));this.search.bind("blur",this.bind(function(E){this.container.removeClass("select2-container-active");this.search.removeClass("select2-focused");this.clearSearch();E.stopImmediatePropagation()}));this.container.delegate(C,"mousedown",this.bind(function(E){if(!this.enabled){return}if(j(E.target).closest(".select2-search-choice").length>0){return}this.clearPlaceholder();this.open();this.focusSearch();E.preventDefault()}));this.container.delegate(C,"focus",this.bind(function(){if(!this.enabled){return}this.container.addClass("select2-container-active");this.dropdown.addClass("select2-drop-active");this.clearPlaceholder()}));this.clearSearch()},enable:function(){if(this.enabled){return}this.parent.enable.apply(this,arguments);this.search.removeAttr("disabled")},disable:function(){if(!this.enabled){return}this.parent.disable.apply(this,arguments);this.search.attr("disabled",true)},initSelection:function(){var 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1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 03 Feb '13

03 Feb '13

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: + ${item} + %endif +</%def> https://bitbucket.org/galaxy/galaxy-central/commits/17c40da527fe/ changeset: 17c40da527fe user: james_taylor date: 2013-02-04 05:21:17 summary: genetrack: Purge all genetrack support (since it no longer exists), other than leaving filetype for backward compatibility affected #: 13 files diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -26,7 +26,6 @@ <converter file="bed_to_summary_tree_converter.xml" target_datatype="summary_tree"/><converter file="bed_to_fli_converter.xml" target_datatype="fli"/> - <display file="genetrack.xml" /><display file="igb/bed.xml" /></datatype><datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true"> @@ -34,7 +33,6 @@ </datatype><datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" /><datatype extension="bed6" type="galaxy.datatypes.interval:Bed6"> - <converter file="bed_to_genetrack_converter.xml" target_datatype="genetrack"/></datatype><datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" /><datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true"> diff -r b7e8d36958522a031a937dc50034b3a57fefe3ed -r 17c40da527fe8fee481ead85bdf8069776fc8f44 display_applications/genetrack.xml --- a/display_applications/genetrack.xml +++ /dev/null @@ -1,18 +0,0 @@ -<display id="genetrack_interval" version="1.0.0" name="view in"> - <link id="genetrack" name="GeneTrack"> - <url target_frame="galaxy_main">http://genetrack.g2.bx.psu.edu/galaxy?filename=${encoded_filename.qp}&h…</url> - <param type="data" name="bed_file" viewable="False" format="bed6,genetrack"/> - <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"> - - - <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> -  - 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"> -  - </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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commit/galaxy-central: james_taylor: templates: Move tool_form templates into templates/webapps/galaxy
by Bitbucket 03 Feb '13

03 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/35e476a0c0c4/ changeset: 35e476a0c0c4 user: james_taylor date: 2013-02-04 05:10:37 summary: templates: Move tool_form templates into templates/webapps/galaxy affected #: 4 files diff -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 -r 35e476a0c0c4a453396010629030c77575fbec95 templates/tool_executed.mako --- a/templates/tool_executed.mako +++ /dev/null @@ -1,70 +0,0 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> -<html> - -<head> -<title>Galaxy</title> -<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> -<script type="text/javascript"> - var inside_galaxy_frameset = false; - - if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history' )}"; - inside_galaxy_frameset = true; - } - - %if trans.user: - if (inside_galaxy_frameset) - { - //parent.frames.galaxy_tools.update_recently_used(); - } - %endif - - if ( parent.handle_minwidth_hint ) { - parent.handle_minwidth_hint( -1 ); - } - - function main() { - // If called from outside the galaxy frameset, redirect there - %if tool.options.refresh: - if ( ! inside_galaxy_frameset ) { - setTimeout( "refresh()", 1000 ); - document.getElementById( "refresh_message" ).style.display = "block"; - } - %endif - } - - function refresh() { - top.location.href = '${h.url_for( "/" )}'; - } - -</script> - -</head> - -<body onLoad="main()"> - -<div class="donemessagelarge"> - -<p>The following job has been successfully added to the queue:</p> - -%for data in out_data.values(): - <div style="padding: 10px"><b> ${data.hid}: ${data.name}</b></div> -%endfor - -<p> -You can check the status of queued jobs and view the resulting -data by refreshing the <b>History</b> pane. When the job has been run -the status will change from 'running' to 'finished' if completed -successfully or 'error' if problems were encountered. -</p> - -%if tool.options.refresh: -<p id="refresh_message" style="display: none;">You are now being redirected back to <a href="${h.url_for( '/' )}">Galaxy</a></div> -%endif - -</div> - -</body> - -</html> diff -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 -r 35e476a0c0c4a453396010629030c77575fbec95 templates/tool_form.mako --- a/templates/tool_form.mako +++ /dev/null @@ -1,357 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/base_panels.mako" import="overlay" /> - -<%def name="stylesheets()"> - ${h.css( "autocomplete_tagging", "base", "panel_layout", "library" )} - <style type="text/css"> - html, body { - background-color: #fff; - } - </style> -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js( "galaxy.panels", "libs/jquery/select2", "libs/jquery/jstorage" )} - <script type="text/javascript"> - $(function() { - $(window).bind("refresh_on_change", function() { - $(':file').each( function() { - var file = $(this); - var file_value = file.val(); - if (file_value) { - // disable file input, since we don't want to upload the file on refresh - var file_name = $(this).attr("name"); - file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } ); - // create a new hidden field which stores the filename and has the original name of the file input - var new_file_input = $(document.createElement('input')); - new_file_input.attr( { "type": "hidden", "value": file_value, "name": file_name } ); - file.after(new_file_input); - } - }); - }); - - // For drilldown parameters: add expand/collapse buttons and collapse initially-collapsed elements - $( 'div.drilldown-container' ).each( function() { - $(this).find('span.form-toggle' ).each( function() { - var show_hide_click_elt = $(this); - var group_id = show_hide_click_elt.attr('id').substring( 0, show_hide_click_elt.attr('id').lastIndexOf( '-click' ) ); - $('#' + group_id + '-container').each( function() { - var show_hide_elt = $(this); - if ( show_hide_click_elt.hasClass( 'toggle-expand' ) ) { - show_hide_elt.hide(); - } - show_hide_click_elt.click( function() { - if ( show_hide_click_elt.hasClass("toggle") ){ - show_hide_click_elt.addClass("toggle-expand"); - show_hide_click_elt.removeClass("toggle"); - show_hide_elt.slideUp( 'fast' ); - } - else { - show_hide_click_elt.addClass("toggle"); - show_hide_click_elt.removeClass("toggle-expand"); - show_hide_elt.slideDown( 'fast' ); - } - }); - }); - }); - }); - - function checkUncheckAll( name, check ) { - $("input[name='" + name + "'][type='checkbox']").attr('checked', !!check); - } - - // Inserts the Select All / Unselect All buttons for checkboxes - $("div.checkUncheckAllPlaceholder").each( function() { - var check_name = $(this).attr("checkbox_name"); - select_link = $("<a class='action-button'></a>").text("Select All").click(function() { - checkUncheckAll(check_name, true); - }); - unselect_link = $("<a class='action-button'></a>").text("Unselect All").click(function() { - checkUncheckAll(check_name, false); - }); - $(this).append(select_link).append(" ").append(unselect_link); - }); - - $(".add-librarydataset").live("click", function() { - var link = $(this); - $.ajax({ - url: "/visualization/list_libraries", - error: function(xhr, ajaxOptions, thrownError) { alert( "Grid failed" ); console.log(xhr, ajaxOptions, thrownError); }, - success: function(table_html) { - show_modal( - "Select Library Dataset", - table_html, { - "Cancel": function() { - hide_modal(); - }, - "Select": function() { - var names = []; - var ids = []; - counter = 1; - $('input[name=ldda_ids]:checked').each(function() { - var name = $.trim( $(this).siblings("label").text() ); - var id = $(this).val(); - names.push( counter + ". " + name ); - counter += 1; - ids.push(id); - }); - link.html( names.join("<br/>") ); - link.siblings("input[type=hidden]").val( ids.join("||") ); - hide_modal(); - } - } - ); - } - }); - }); - }); - - %if not add_frame.debug: - if( window.name != "galaxy_main" ) { - location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' ); - } - %endif - - </script> - -</%def> - -<%def name="do_inputs( inputs, tool_state, errors, prefix, other_values=None )"> - <% - from galaxy.util.expressions import ExpressionContext - other_values = ExpressionContext( tool_state, other_values ) - %> - %for input_index, input in enumerate( inputs.itervalues() ): - %if not input.visible: - <% pass %> - %elif input.type == "repeat": - <div class="repeat-group"> - <div class="form-title-row"><strong>${input.title_plural}</strong> - %if input.help: - <div class="toolParamHelp" style="clear: both;"> - ${input.help} - </div> - %endif - </div> - <% - repeat_state = tool_state[input.name] - num_repeats = len( repeat_state ) - %> - %for i in range( num_repeats ): - <div class="repeat-group-item"> - <% - if input.name in errors: - rep_errors = errors[input.name][i] - else: - rep_errors = dict() - index = repeat_state[i]['__index__'] - %> - <div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div> - ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} - %if input.min < num_repeats: - <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> - %endif - </div> - %if rep_errors.has_key( '__index__' ): - <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div> - %endif - %endfor - %if input.max > num_repeats: - <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> - %endif - </div> - %elif input.type == "conditional": - <% - group_state = tool_state[input.name] - group_errors = errors.get( input.name, {} ) - current_case = group_state['__current_case__'] - group_prefix = prefix + input.name + "|" - %> - %if input.value_ref_in_group: - ${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )} - %endif - ${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )} - %elif input.type == "upload_dataset": - %if input.get_datatype( trans, other_values ).composite_type is None: #have non-composite upload appear as before - <% - if input.name in errors: - rep_errors = errors[input.name][0] - else: - rep_errors = dict() - %> - ${do_inputs( input.inputs, tool_state[input.name][0], rep_errors, prefix + input.name + "_" + str( 0 ) + "|", other_values )} - %else: - <div class="repeat-group"> - <div class="form-title-row"><strong>${input.group_title( other_values )}</strong></div> - <% - repeat_state = tool_state[input.name] - %> - %for i in range( len( repeat_state ) ): - <div class="repeat-group-item"> - <% - if input.name in errors: - rep_errors = errors[input.name][i] - else: - rep_errors = dict() - index = repeat_state[i]['__index__'] - %> - <div class="form-title-row"><strong>File Contents for ${input.title_by_index( trans, i, other_values )}</strong></div> - ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} - ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> - </div> - %endfor - ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> - </div> - %endif - %else: - ${row_for_param( prefix, input, tool_state, errors, other_values )} - %endif - %endfor -</%def> - -<%def name="row_for_param( prefix, param, parent_state, parent_errors, other_values )"> - <% - if parent_errors.has_key( param.name ): - cls = "form-row form-row-error" - else: - cls = "form-row" - - label = param.get_label() - - field = param.get_html_field( trans, parent_state[ param.name ], other_values ) - field.refresh_on_change = param.refresh_on_change - - # Field may contain characters submitted by user and these characters may be unicode; handle non-ascii characters gracefully. - field_html = field.get_html( prefix ) - if type( field_html ) is not unicode: - field_html = unicode( field_html, 'utf-8', 'replace' ) - - if param.type == "hidden": - return field_html - %> - <div class="${cls}"> - %if label: - <label for="${param.name}">${label}:</label> - %endif - <div class="form-row-input">${field_html}</div> - %if parent_errors.has_key( param.name ): - <div class="form-row-error-message"> - <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${parent_errors[param.name]}</span></div> - </div> - %endif - - %if param.help: - <div class="toolParamHelp" style="clear: both;"> - ${param.help} - </div> - %endif - - <div style="clear: both;"></div> - - </div> -</%def> - -<% overlay(visible=False) %> - -%if add_frame.from_noframe: - <div class="warningmessage"> - <strong>Welcome to Galaxy</strong> - <hr/> - It appears that you found this tool from a link outside of Galaxy. - If you're not familiar with Galaxy, please consider visiting the - <a href="${h.url_for( controller='root' )}" target="_top">welcome page</a>. - To learn more about what Galaxy is and what it can do for you, please visit - the <a href="${add_frame.wiki_url}" target="_top">Galaxy wiki</a>. - </div> - <br/> -%endif - -<% - # Render an error message if a dynamically generated select list is missing a required - # index file or entry in the tool_data_table_conf.xml file. - message = "" - params_with_missing_data_table_entry = tool.params_with_missing_data_table_entry - params_with_missing_index_file = tool.params_with_missing_index_file - if params_with_missing_data_table_entry: - param = params_with_missing_data_table_entry[0] - message += "Data table named '%s' is required by tool but not configured. " % param.options.missing_tool_data_table_name - if tool.params_with_missing_index_file: - param = params_with_missing_index_file[0] - message += "Index file named '%s' is required by tool but not available. " % param.options.missing_index_file - - # Handle calculating the redirect url for the special case where we have nginx proxy - # upload and need to do url_for on the redirect portion of the tool action. - try: - tool_url = h.url_for(tool.action) - except AttributeError: - assert len(tool.action) == 2 - tool_url = tool.action[0] + h.url_for(tool.action[1]) -%> - -<% - # Name of the tool in lower case - low_tool_name = tool.name.lower() -%> - -%if tool_id_version_message: - ${render_msg( tool_id_version_message, 'warning' )} -%endif - -<div class="toolForm" id="${tool.id}"> - <form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}"> - %if tool.has_multiple_pages: - <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages}) - %elif not tool_version_select_field: - <div class="toolFormTitle">${tool.name} (version ${tool.version}) - %else: - <div class="toolFormTitle">${tool.name} ${tool_version_select_field.get_html()} - %endif - %if trans.app.config.biostar: -  - <a href="${trans.app.config.biostar}/new/post/tagged/${low_tool_name}" target="galaxy_main" class="icon-button general-question tooltip close-side-panels" data-original-title="Ask a tool related question"></a> - <a href="${trans.app.config.biostar}/show/tag/${low_tool_name}/" target="galaxy_main" class="icon-button tag-question tooltip close-side-panels" data-original-title="See tool related posts" ></a> -  - %endif - </div> - <div class="toolFormBody"> - <input type="hidden" name="refresh" value="refresh"> - <input type="hidden" name="tool_id" value="${tool.id}"> - <input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> - %if tool.display_by_page[tool_state.page]: - ${trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )} - <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute"> - %else: - ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, errors, "" )} - <div class="form-row form-actions"> - %if tool_state.page == tool.last_page: - <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute"> - %else: - <input type="submit" class="btn btn-primary" name="runtool_btn" value="Next step"> - %endif - </div> - %endif - </div> - </form> -</div> -%if tool.help: - <div class="toolHelp"> - <div class="toolHelpBody"> - <% - if tool.has_multiple_pages: - tool_help = tool.help_by_page[tool_state.page] - else: - tool_help = tool.help - - # Help is Mako template, so render using current static path. - tool_help = tool_help.render( static_path=h.url_for( '/static' ) ) - - # Convert to unicode to display non-ascii characters. - if type( tool_help ) is not unicode: - tool_help = unicode( tool_help, 'utf-8') - %> - ${tool_help} - </div> - </div> -%endif diff -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 -r 35e476a0c0c4a453396010629030c77575fbec95 templates/webapps/galaxy/tool_executed.mako --- /dev/null +++ b/templates/webapps/galaxy/tool_executed.mako @@ -0,0 +1,70 @@ +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> +<html> + +<head> +<title>Galaxy</title> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> +<script type="text/javascript"> + var inside_galaxy_frameset = false; + + if ( parent.frames && parent.frames.galaxy_history ) { + parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history' )}"; + inside_galaxy_frameset = true; + } + + %if trans.user: + if (inside_galaxy_frameset) + { + //parent.frames.galaxy_tools.update_recently_used(); + } + %endif + + if ( parent.handle_minwidth_hint ) { + parent.handle_minwidth_hint( -1 ); + } + + function main() { + // If called from outside the galaxy frameset, redirect there + %if tool.options.refresh: + if ( ! inside_galaxy_frameset ) { + setTimeout( "refresh()", 1000 ); + document.getElementById( "refresh_message" ).style.display = "block"; + } + %endif + } + + function refresh() { + top.location.href = '${h.url_for( "/" )}'; + } + +</script> + +</head> + +<body onLoad="main()"> + +<div class="donemessagelarge"> + +<p>The following job has been successfully added to the queue:</p> + +%for data in out_data.values(): + <div style="padding: 10px"><b> ${data.hid}: ${data.name}</b></div> +%endfor + +<p> +You can check the status of queued jobs and view the resulting +data by refreshing the <b>History</b> pane. When the job has been run +the status will change from 'running' to 'finished' if completed +successfully or 'error' if problems were encountered. +</p> + +%if tool.options.refresh: +<p id="refresh_message" style="display: none;">You are now being redirected back to <a href="${h.url_for( '/' )}">Galaxy</a></div> +%endif + +</div> + +</body> + +</html> diff -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 -r 35e476a0c0c4a453396010629030c77575fbec95 templates/webapps/galaxy/tool_form.mako --- /dev/null +++ b/templates/webapps/galaxy/tool_form.mako @@ -0,0 +1,357 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/base_panels.mako" import="overlay" /> + +<%def name="stylesheets()"> + ${h.css( "autocomplete_tagging", "base", "panel_layout", "library" )} + <style type="text/css"> + html, body { + background-color: #fff; + } + </style> +</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js( "galaxy.panels", "libs/jquery/select2", "libs/jquery/jstorage" )} + <script type="text/javascript"> + $(function() { + $(window).bind("refresh_on_change", function() { + $(':file').each( function() { + var file = $(this); + var file_value = file.val(); + if (file_value) { + // disable file input, since we don't want to upload the file on refresh + var file_name = $(this).attr("name"); + file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } ); + // create a new hidden field which stores the filename and has the original name of the file input + var new_file_input = $(document.createElement('input')); + new_file_input.attr( { "type": "hidden", "value": file_value, "name": file_name } ); + file.after(new_file_input); + } + }); + }); + + // For drilldown parameters: add expand/collapse buttons and collapse initially-collapsed elements + $( 'div.drilldown-container' ).each( function() { + $(this).find('span.form-toggle' ).each( function() { + var show_hide_click_elt = $(this); + var group_id = show_hide_click_elt.attr('id').substring( 0, show_hide_click_elt.attr('id').lastIndexOf( '-click' ) ); + $('#' + group_id + '-container').each( function() { + var show_hide_elt = $(this); + if ( show_hide_click_elt.hasClass( 'toggle-expand' ) ) { + show_hide_elt.hide(); + } + show_hide_click_elt.click( function() { + if ( show_hide_click_elt.hasClass("toggle") ){ + show_hide_click_elt.addClass("toggle-expand"); + show_hide_click_elt.removeClass("toggle"); + show_hide_elt.slideUp( 'fast' ); + } + else { + show_hide_click_elt.addClass("toggle"); + show_hide_click_elt.removeClass("toggle-expand"); + show_hide_elt.slideDown( 'fast' ); + } + }); + }); + }); + }); + + function checkUncheckAll( name, check ) { + $("input[name='" + name + "'][type='checkbox']").attr('checked', !!check); + } + + // Inserts the Select All / Unselect All buttons for checkboxes + $("div.checkUncheckAllPlaceholder").each( function() { + var check_name = $(this).attr("checkbox_name"); + select_link = $("<a class='action-button'></a>").text("Select All").click(function() { + checkUncheckAll(check_name, true); + }); + unselect_link = $("<a class='action-button'></a>").text("Unselect All").click(function() { + checkUncheckAll(check_name, false); + }); + $(this).append(select_link).append(" ").append(unselect_link); + }); + + $(".add-librarydataset").live("click", function() { + var link = $(this); + $.ajax({ + url: "/visualization/list_libraries", + error: function(xhr, ajaxOptions, thrownError) { alert( "Grid failed" ); console.log(xhr, ajaxOptions, thrownError); }, + success: function(table_html) { + show_modal( + "Select Library Dataset", + table_html, { + "Cancel": function() { + hide_modal(); + }, + "Select": function() { + var names = []; + var ids = []; + counter = 1; + $('input[name=ldda_ids]:checked').each(function() { + var name = $.trim( $(this).siblings("label").text() ); + var id = $(this).val(); + names.push( counter + ". " + name ); + counter += 1; + ids.push(id); + }); + link.html( names.join("<br/>") ); + link.siblings("input[type=hidden]").val( ids.join("||") ); + hide_modal(); + } + } + ); + } + }); + }); + }); + + %if not add_frame.debug: + if( window.name != "galaxy_main" ) { + location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' ); + } + %endif + + </script> + +</%def> + +<%def name="do_inputs( inputs, tool_state, errors, prefix, other_values=None )"> + <% + from galaxy.util.expressions import ExpressionContext + other_values = ExpressionContext( tool_state, other_values ) + %> + %for input_index, input in enumerate( inputs.itervalues() ): + %if not input.visible: + <% pass %> + %elif input.type == "repeat": + <div class="repeat-group"> + <div class="form-title-row"><strong>${input.title_plural}</strong> + %if input.help: + <div class="toolParamHelp" style="clear: both;"> + ${input.help} + </div> + %endif + </div> + <% + repeat_state = tool_state[input.name] + num_repeats = len( repeat_state ) + %> + %for i in range( num_repeats ): + <div class="repeat-group-item"> + <% + if input.name in errors: + rep_errors = errors[input.name][i] + else: + rep_errors = dict() + index = repeat_state[i]['__index__'] + %> + <div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div> + ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} + %if input.min < num_repeats: + <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + %endif + </div> + %if rep_errors.has_key( '__index__' ): + <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div> + %endif + %endfor + %if input.max > num_repeats: + <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> + %endif + </div> + %elif input.type == "conditional": + <% + group_state = tool_state[input.name] + group_errors = errors.get( input.name, {} ) + current_case = group_state['__current_case__'] + group_prefix = prefix + input.name + "|" + %> + %if input.value_ref_in_group: + ${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )} + %endif + ${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )} + %elif input.type == "upload_dataset": + %if input.get_datatype( trans, other_values ).composite_type is None: #have non-composite upload appear as before + <% + if input.name in errors: + rep_errors = errors[input.name][0] + else: + rep_errors = dict() + %> + ${do_inputs( input.inputs, tool_state[input.name][0], rep_errors, prefix + input.name + "_" + str( 0 ) + "|", other_values )} + %else: + <div class="repeat-group"> + <div class="form-title-row"><strong>${input.group_title( other_values )}</strong></div> + <% + repeat_state = tool_state[input.name] + %> + %for i in range( len( repeat_state ) ): + <div class="repeat-group-item"> + <% + if input.name in errors: + rep_errors = errors[input.name][i] + else: + rep_errors = dict() + index = repeat_state[i]['__index__'] + %> + <div class="form-title-row"><strong>File Contents for ${input.title_by_index( trans, i, other_values )}</strong></div> + ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} + ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + </div> + %endfor + ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> + </div> + %endif + %else: + ${row_for_param( prefix, input, tool_state, errors, other_values )} + %endif + %endfor +</%def> + +<%def name="row_for_param( prefix, param, parent_state, parent_errors, other_values )"> + <% + if parent_errors.has_key( param.name ): + cls = "form-row form-row-error" + else: + cls = "form-row" + + label = param.get_label() + + field = param.get_html_field( trans, parent_state[ param.name ], other_values ) + field.refresh_on_change = param.refresh_on_change + + # Field may contain characters submitted by user and these characters may be unicode; handle non-ascii characters gracefully. + field_html = field.get_html( prefix ) + if type( field_html ) is not unicode: + field_html = unicode( field_html, 'utf-8', 'replace' ) + + if param.type == "hidden": + return field_html + %> + <div class="${cls}"> + %if label: + <label for="${param.name}">${label}:</label> + %endif + <div class="form-row-input">${field_html}</div> + %if parent_errors.has_key( param.name ): + <div class="form-row-error-message"> + <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${parent_errors[param.name]}</span></div> + </div> + %endif + + %if param.help: + <div class="toolParamHelp" style="clear: both;"> + ${param.help} + </div> + %endif + + <div style="clear: both;"></div> + + </div> +</%def> + +<% overlay(visible=False) %> + +%if add_frame.from_noframe: + <div class="warningmessage"> + <strong>Welcome to Galaxy</strong> + <hr/> + It appears that you found this tool from a link outside of Galaxy. + If you're not familiar with Galaxy, please consider visiting the + <a href="${h.url_for( controller='root' )}" target="_top">welcome page</a>. + To learn more about what Galaxy is and what it can do for you, please visit + the <a href="${add_frame.wiki_url}" target="_top">Galaxy wiki</a>. + </div> + <br/> +%endif + +<% + # Render an error message if a dynamically generated select list is missing a required + # index file or entry in the tool_data_table_conf.xml file. + message = "" + params_with_missing_data_table_entry = tool.params_with_missing_data_table_entry + params_with_missing_index_file = tool.params_with_missing_index_file + if params_with_missing_data_table_entry: + param = params_with_missing_data_table_entry[0] + message += "Data table named '%s' is required by tool but not configured. " % param.options.missing_tool_data_table_name + if tool.params_with_missing_index_file: + param = params_with_missing_index_file[0] + message += "Index file named '%s' is required by tool but not available. " % param.options.missing_index_file + + # Handle calculating the redirect url for the special case where we have nginx proxy + # upload and need to do url_for on the redirect portion of the tool action. + try: + tool_url = h.url_for(tool.action) + except AttributeError: + assert len(tool.action) == 2 + tool_url = tool.action[0] + h.url_for(tool.action[1]) +%> + +<% + # Name of the tool in lower case + low_tool_name = tool.name.lower() +%> + +%if tool_id_version_message: + ${render_msg( tool_id_version_message, 'warning' )} +%endif + +<div class="toolForm" id="${tool.id}"> + <form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}"> + %if tool.has_multiple_pages: + <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages}) + %elif not tool_version_select_field: + <div class="toolFormTitle">${tool.name} (version ${tool.version}) + %else: + <div class="toolFormTitle">${tool.name} ${tool_version_select_field.get_html()} + %endif + %if trans.app.config.biostar: +  + <a href="${trans.app.config.biostar}/new/post/tagged/${low_tool_name}" target="galaxy_main" class="icon-button general-question tooltip close-side-panels" data-original-title="Ask a tool related question"></a> + <a href="${trans.app.config.biostar}/show/tag/${low_tool_name}/" target="galaxy_main" class="icon-button tag-question tooltip close-side-panels" data-original-title="See tool related posts" ></a> +  + %endif + </div> + <div class="toolFormBody"> + <input type="hidden" name="refresh" value="refresh"> + <input type="hidden" name="tool_id" value="${tool.id}"> + <input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> + %if tool.display_by_page[tool_state.page]: + ${trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )} + <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute"> + %else: + ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, errors, "" )} + <div class="form-row form-actions"> + %if tool_state.page == tool.last_page: + <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute"> + %else: + <input type="submit" class="btn btn-primary" name="runtool_btn" value="Next step"> + %endif + </div> + %endif + </div> + </form> +</div> +%if tool.help: + <div class="toolHelp"> + <div class="toolHelpBody"> + <% + if tool.has_multiple_pages: + tool_help = tool.help_by_page[tool_state.page] + else: + tool_help = tool.help + + # Help is Mako template, so render using current static path. + tool_help = tool_help.render( static_path=h.url_for( '/static' ) ) + + # Convert to unicode to display non-ascii characters. + if type( tool_help ) is not unicode: + tool_help = unicode( tool_help, 'utf-8') + %> + ${tool_help} + </div> + </div> +%endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: james_taylor: template: Move templates used *only* by the galaxy webapp into templates/webapps/galaxy
by Bitbucket 03 Feb '13

03 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4c6e63dc04c9/ changeset: 4c6e63dc04c9 user: james_taylor date: 2013-02-04 05:07:11 summary: template: Move templates used *only* by the galaxy webapp into templates/webapps/galaxy affected #: 258 files diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/cloud/index.mako --- a/templates/cloud/index.mako +++ /dev/null @@ -1,291 +0,0 @@ -<%inherit file="/webapps/galaxy/base_panels.mako"/> - -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=False - self.active_view="shared" - self.message_box_visible=False -%> -</%def> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "autocomplete_tagging" )} - <style type="text/css"> - #new_history_p{ - line-height:2.5em; - margin:0em 0em .5em 0em; - } - #new_history_cbx{ - margin-right:.5em; - } - #new_history_input{ - display:none; - line-height:1em; - } - #ec_button_container{ - float:right; - } - #hidden_options{ - display:none; - } - div.toolForm{ - margin-top: 10px; - margin-bottom: 10px; - } - div.toolFormTitle{ - cursor:pointer; - } - .title_ul_text{ - text-decoration:underline; - } - .step-annotation { - margin-top: 0.25em; - font-weight: normal; - font-size: 97%; - } - .workflow-annotation { - margin-bottom: 1em; - } - #loading_indicator{ - position:fixed; - top:40px; - } - </style> -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - var ACCOUNT_URL = "${h.url_for( controller='/cloudlaunch', action='get_account_info')}"; - var PKEY_DL_URL = "${h.url_for( controller='/cloudlaunch', action='get_pkey')}"; - var cloudlaunch_clusters = []; - - $(document).ready(function(){ - $('#id_existing_instance').change(function(){ - var ei_name = $(this).val(); - if (ei_name === "New Cluster"){ - //For new instances, need to see the cluster name field. - $('#id_cluster_name').val("New Cluster") - $('#cluster_name_wrapper').show('fast'); - }else{ - //Hide the Cluster Name field, but set the value - $('#id_cluster_name').val($(this).val()); - $('#cluster_name_wrapper').hide('fast'); - } - }); - //When id_secret and id_key are complete, submit to get_account_info - $("#id_secret, #id_key_id").bind("paste input propertychange", function(){ - secret_el = $("#id_secret"); - key_el = $("#id_key_id"); - if (secret_el.val().length === 40 && key_el.val().length === 20){ - //Submit these to get_account_info, unhide fields, and update as appropriate - $.ajax({type: "POST", - url: ACCOUNT_URL, - dataType: 'json', - data: {key_id: key_el.val(),secret:secret_el.val()}, - success: function(result){ - cloudlaunch_clusters = result.clusters; - var kplist = $("#id_keypair"); - var clusterlist = $("#id_existing_instance"); - kplist.find('option').remove(); - clusterlist.find('option').remove(); - //Update fields with appropriate elements - clusterlist.append($('<option/>').val('New Cluster').text('New Cluster')); - if (_.size(result.clusters) > 0){ - _.each(result.clusters, function(cluster, index){ - clusterlist.append($('<option/>').val(cluster.name).text(cluster.name)); - }); - $('#existing_instance_wrapper').show(); - } - if (!_.include(result.keypairs, '${default_keypair}')){ - kplist.append($('<option/>').val('${default_keypair}').text('Create New - ${default_keypair}')); - } - _.each(result.keypairs, function(keypair, index){ - kplist.append($('<option/>').val(keypair).text(keypair)); - }); - $('#hidden_options').show('fast'); - } - }); - } - }); - $('#loading_indicator').ajaxStart(function(){ - $(this).show('fast'); - }).ajaxStop(function(){ - $(this).hide('fast'); - }); - $('form').ajaxForm({ - type: 'POST', - dataType: 'json', - beforeSubmit: function(data, form){ - if ($('#id_password').val() != $('#id_password_confirm').val()){ - //Passwords don't match. - form.prepend('<div class="errormessage">Passwords do not match</div>'); - return false; - }else{ - //Clear errors - $('.errormessage').remove() - //Hide the form, show pending box with spinner. - $('#launchFormContainer').hide('fast'); - $('#responsePanel').show('fast'); - } - //Dig up zone info for selected cluster, set hidden input. - //This is not necessary to present to the user though the interface may prove useful. - var ei_val = _.find(data, function(f_obj){return f_obj.name === 'existing_instance'}); - if( ei_val && (ei_val.value !== "New Cluster")){ - var cluster = _.find(cloudlaunch_clusters, function(cluster){return cluster.name === ei_val.value}); - var zdata = _.find(data, function(f_obj){return f_obj.name === 'zone'}); - zdata.value = cluster.zone; - } - }, - success: function(data){ - //Success Message, link to key download if required, link to server itself. - $('#launchPending').hide('fast'); - //Set appropriate fields (dns, key, ami) and then display. - if(data.kp_material_tag){ - var kp_download_link = $('<a/>').attr('href', PKEY_DL_URL + '?kp_material_tag=' + data.kp_material_tag) - .attr('target','_blank') - .text("Download your key now"); - $('#keypairInfo').append(kp_download_link); - $('#keypairInfo').show(); - } - $('.kp_name').text(data.kp_name); - $('#instance_id').text(data.instance_id); - $('#image_id').text(data.image_id); - $('#instance_link').html($('<a/>') - .attr('href', 'http://' + data.public_dns_name + '/cloud') - .attr('target','_blank') - .text(data.public_dns_name + '/cloud')); - $('#instance_dns').text(data.public_dns_name); - $('#launchSuccess').show('fast'); - }, - error: function(jqXHR, textStatus, errorThrown){ - $('#launchFormContainer').prepend('<div class="errormessage">' + errorThrown + " : " + jqXHR.responseText + '</div>'); - $('#responsePanel').hide('fast'); - $('#launchFormContainer').show('fast'); - } - }); - }); - </script> -</%def> - -<%def name="center_panel()"> - <div style="overflow: auto; height: 100%;"> - <div class="page-container" style="padding: 10px;"> - <div id="loading_indicator"></div> - <h2>Launch a Galaxy Cloud Instance</h2> - <div id="launchFormContainer" class="toolForm"> - <form id="cloudlaunch_form" action="${h.url_for( controller='/cloudlaunch', action='launch_instance')}" method="post"> - - <p>To launch a Galaxy Cloud Cluster, enter your AWS Secret Key ID, and Secret Key. Galaxy will use - these to present appropriate options for launching your cluster. Note that using this form to - launch computational resources in the Amazon Cloud will result in costs to the account indicated - above. See <a href="http://aws.amazon.com/ec2/pricing/">Amazon's pricing</a> for more information. - options for launching your cluster.</p></p> - - <div class="form-row"> - <label for="id_key_id">Key ID</label> - <input type="text" size="30" maxlength="20" name="key_id" id="id_key_id" value=""/><br/> - <div class="toolParamHelp"> - This is the text string that uniquely identifies your account, found in the - <a href="https://portal.aws.amazon.com/gp/aws/securityCredentials">Security Credentials section of the AWS Console</a>. - </div> - </div> - - <div class="form-row"> - <label for="id_secret">Secret Key</label> - <input type="text" size="50" maxlength="40" name="secret" id="id_secret" value=""/><br/> - <div class="toolParamHelp"> - This is your AWS Secret Key, also found in the <a href="https://portal.aws.amazon.com/gp/aws/securityCredentials">Security -Credentials section of the AWS Console</a>. </div> - </div> - - <div id="hidden_options"> - <div id='existing_instance_wrapper' style="display:none;" class="form-row"> - <label for="id_existing_instance">Instances in your account</label> - <select name="existing_instance" id="id_existing_instance"> - </select> - <input id='id_zone' type='hidden' name='zone' value=''/> - </div> - <div id='cluster_name_wrapper' class="form-row"> - <label for="id_cluster_name">Cluster Name</label> - <input type="text" size="40" class="text-and-autocomplete-select" name="cluster_name" id="id_cluster_name"/><br/> - <div class="toolParamHelp"> - This is the name for your cluster. You'll use this when you want to restart. - </div> - </div> - - <div class="form-row"> - <label for="id_password">Cluster Password</label> - <input type="password" size="40" name="password" id="id_password"/><br/> - </div> - - <div class="form-row"> - <label for="id_password_confirm">Cluster Password - Confirmation</label> - <input type="password" size="40" name="password_confirm" id="id_password_confirm"/><br/> - </div> - - - <div class="form-row"> - <label for="id_keypair">Key Pair</label> - <select name="keypair" id="id_keypair"> - <option name="Create" value="cloudman_keypair">cloudman_keypair</option> - </select> - </div> - - %if share_string: - <input type='hidden' name='share_string' value='${share_string}'/> - %else: -  - <div class="form-row" style="display:none;"> - <label for="id_share_string">Instance Share String (optional)</label> - <input type="text" size="120" name="share_string" id="id_share_string"/><br/> - </div> - %endif - - <div class="form-row"> - <label for="id_instance_type">Instance Type</label> - <select name="instance_type" id="id_instance_type"> - <option value="m1.large">Large</option> - <option value="m1.xlarge">Extra Large</option> - <option value="m2.4xlarge">High-Memory Quadruple Extra Large</option> - </select> - </div> - <div class="form-row"> - <p>Requesting the instance may take a moment, please be patient. Do not refresh your browser or navigate away from the page</p> - <input type="submit" value="Submit" id="id_submit"/> - </div> - </div> - <div class="form-row"> - <div id="loading_indicator" style="position:relative;left:10px;right:0px"></div> - </div> - </form> - </div> - <div id="responsePanel" class="toolForm" style="display:none;"> - <div id="launchPending">Launch Pending, please be patient.</div> - <div id="launchSuccess" style="display:none;"> - <div id="keypairInfo" style="display:none;margin-bottom:20px;"> - <h3>Very Important Key Pair Information</h3> - <p>A new key pair named <strong><span class="kp_name">kp_name</span></strong> has been created in your AWS - account and will be used to access this instance via ssh. It is - <strong>very important</strong> that you save the following private key - as it is not saved on this Galaxy instance and will be permanently lost if not saved. Additionally, this link will - only allow a single download, after which the key is removed from the Galaxy server permanently.<br/> - </div> - <div> - <h3>Access Information</h3> - <ul> - <li>Your instance '<span id="instance_id">undefined</span>' has been successfully launched using the - '<span id="image_id">undefined</span>' AMI.</li> - <li>While it may take a few moments to boot, you will be able to access the cloud control - panel at <span id="instance_link">undefined.</span>.</li> - <li>SSH access is also available using your private key. From the terminal, you would execute something like:</br>    `ssh -i <span class="kp_name">undefined</span>.pem ubuntu@<span -id="instance_dns">undefined</span>`</li> - </ul> - </div> - </div> - </div> - </div> -</%def> - diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/cloud/run.mako --- a/templates/cloud/run.mako +++ /dev/null @@ -1,41 +0,0 @@ -<%inherit file="/webapps/galaxy/base_panels.mako"/> - -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=False - self.active_view="shared" - self.message_box_visible=False -%> -</%def> - - -<%def name="center_panel()"> - <div style="overflow: auto; height: 100%;"> - <div class="page-container" style="padding: 10px;"> - <h2>Launching a Galaxy Cloud Instance</h2> -%if error: - <p>${error}</p> -%elif instance: - %if kp_material: - <h3>Very Important Key Pair Information</h3> - <p>A new key pair named '${kp_name}' has been created in your AWS - account and will be used to access this instance via ssh. It is - <strong>very important</strong> that you save the following private key - as it is not saved on this Galaxy instance and will be permanently lost - once you leave this page. To do this, save the following key block as - a plain text file named '${kp_name}'.</p> - <pre>${kp_material}</pre> - %endif - <p>The instance '${instance.id} has been successfully launched using the - '${instance.image_id}' AMI.<br/> Access it at <a - href="http://${instance.public_dns_name}">http://${instance.public_dns_name}</a></p> - <p>SSH access is available using your private key '${kp_name}'.</p> -%else: - <p> Unknown failure, no instance. Please refer to your AWS console at <a - href="https://console.aws.amazon.com">https://console.aws.amazon.com</a></p> -%endif - </div> - </div> -</%def> - diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/copy_view.mako --- a/templates/dataset/copy_view.mako +++ /dev/null @@ -1,141 +0,0 @@ -<%inherit file="/base.mako"/> -<%def name="title()">Copy History Items</%def> - -<%def name="javascripts()"> - - ${parent.javascripts()} - - <script type="text/javascript"> - $(function() { - $("#select-multiple").click(function() { - $("#single-dest-select").val(""); - $("#single-destination").hide(); - $("#multiple-destination").show(); - }); - }); - %if 'history' in refresh_frames: - if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; - if ( parent.force_right_panel ) { - parent.force_right_panel( 'show' ); - } - } - %endif - </script> - -</%def> - -%if error_msg: - <p> - <div class="errormessage">${error_msg}</div> - <div style="clear: both"></div> - </p> -%endif -%if done_msg: - <p> - <div class="donemessage">${done_msg}</div> - <div style="clear: both"></div> - </p> -%endif -<p> - <div class="infomessage">Copy any number of history items from one history to another.</div> - <div style="clear: both"></div> -</p> -<p> - <form method="post"> - <div class="toolForm" style="float: left; width: 45%; padding: 0px;"> - <div class="toolFormTitle">Source History:<br /> - <select id="source_history" name="source_history" refresh_on_change="true" style="font-weight: normal;"> - %for i, hist in enumerate(target_histories): - <% - selected = "" - current_history_text = "" - if hist == source_history: - selected = "selected='selected'" - if hist == current_history: - current_history_text = " (current history)" - - %> - <option value="${trans.security.encode_id(hist.id)}" ${selected}> - ${i + 1}: ${h.truncate(util.unicodify( hist.name ), 30)}${current_history_text} - </option> - %endfor - </select> - </div> - <div class="toolFormBody"> - %if len(source_datasets) > 0: - %for data in source_datasets: - <% - checked = "" - encoded_id = trans.security.encode_id(data.id) - if data.id in source_dataset_ids: - checked = " checked='checked'" - %> - <div class="form-row"> - <input type="checkbox" name="source_dataset_ids" id="dataset_${encoded_id}" value="${encoded_id}"${checked}/> - <label for="dataset_${encoded_id}" style="display: inline;font-weight:normal;"> ${data.hid}: ${h.to_unicode(data.name)}</label> - </div> - %endfor - %else: - <div class="form-row">This history has no datasets.</div> - %endif - </div> - </div> - <div style="float: left; padding-left: 10px; font-size: 36px;">→</div> - <div class="toolForm" style="float: right; width: 45%; padding: 0px;"> - <div class="toolFormTitle">Destination History:</div> - <div class="toolFormBody"> - <div class="form-row" id="single-destination"> - <select id="single-dest-select" name="target_history_id"> - <option value=""></option> - %for i, hist in enumerate(target_histories): - <% - encoded_id = trans.security.encode_id(hist.id) - source_history_text = "" - selected = "" - if hist == source_history: - source_history_text = " (source history)" - if encoded_id == target_history_id: - selected = " selected='selected'" - %> - <option value="${encoded_id}"${selected}>${i + 1}: ${h.truncate( util.unicodify( hist.name ), 30)}${source_history_text}</option> - %endfor - </select><br /><br /> - <a style="margin-left: 10px;" href="javascript:void(0);" id="select-multiple">Choose multiple histories</a> - </div> - <div id="multiple-destination" style="display: none;"> - %for i, hist in enumerate( target_histories ): - <% - cur_history_text = "" - encoded_id = trans.security.encode_id(hist.id) - if hist == source_history: - cur_history_text = " <strong>(source history)</strong>" - %> - <div class="form-row"> - <input type="checkbox" name="target_history_ids" id="hist_${encoded_id}" value="${encoded_id}"/> - <label for="hist_${encoded_id}" style="display: inline; font-weight:normal;">${i + 1}: ${ util.unicodify( hist.name ) }${cur_history_text}</label> - </div> - %endfor - </div> - %if trans.get_user(): - <% - checked = "" - if "create_new_history" in target_history_ids: - checked = " checked='checked'" - %> - <hr /> - <div style="text-align: center; color: #888;">— OR —</div> - <div class="form-row"> - <label for="new_history_name" style="display: inline; font-weight:normal;">New history named:</label> - <input type="textbox" name="new_history_name" /> - </div> - %endif - </div> - </div> - <div style="clear: both"></div> - <div class="form-row" align="center"> - <input type="submit" class="primary-button" name="do_copy" value="Copy History Items"/> - </div> - </form> - </div> -</p> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/display.mako --- a/templates/dataset/display.mako +++ /dev/null @@ -1,111 +0,0 @@ -## Because HDAs do not have many of the properties that other sharable items have, we need to override most of the default code for display. -<%inherit file="/display_base.mako"/> -<%namespace file="/display_common.mako" import="*" /> -<%namespace file="/tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" /> - -<%def name="javascripts()"> - ${parent.javascripts()} -</%def> - -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=True - self.message_box_visible=False - self.active_view="user" - self.overlay_visible=False -%> -</%def> - -<%def name="title()"> - Galaxy | ${get_class_display_name( item.__class__ )} | ${get_item_name( item ) | h} -</%def> - -<%def name="render_item_links( data )"> - ## Provide links to save data and import dataset. - <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( data.id ), to_ext=data.ext )}" class="icon-button disk tooltip" title="Save dataset"></a> - <a - href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( data.id ) )}" - class="icon-button import tooltip" - title="Import dataset"></a> -</%def> - -<%def name="render_item( data, data_to_render )"> - %if truncated: - <div class="warningmessagelarge"> - This dataset is large and only the first megabyte is shown below. | - <a href="${h.url_for( controller='dataset', action='display_by_username_and_slug', username=data.history.user.username, slug=trans.security.encode_id( data.id ), preview=False )}">Show all</a> - </div> - %endif - ## TODO: why is the default font size so small? - <pre style="font-size: 135%">${ data_to_render | h }</pre> -</%def> - - -<%def name="center_panel()"> - <div class="unified-panel-header" unselectable="on"> - <div class="unified-panel-header-inner"> - ${get_class_display_name( item.__class__ )} - | ${get_item_name( item ) | h} - </div> - </div> - - <div class="unified-panel-body"> - <div style="overflow: auto; height: 100%;"> - <div class="page-body"> - <div style="float: right"> - ${self.render_item_links( item )} - </div> - <div> - ${self.render_item_header( item )} - </div> - - ${self.render_item( item, item_data )} - </div> - </div> - </div> -</%def> - -<%def name="right_panel()"> - <div class="unified-panel-header" unselectable="on"> - <div class="unified-panel-header-inner"> - About this ${get_class_display_name( item.__class__ )} - </div> - </div> - - <div class="unified-panel-body"> - <div style="overflow: auto; height: 100%;"> - <div style="padding: 10px;"> - <h4>Author</h4> - - <p>${item.history.user.username | h}</p> - - <div><img src="https://secure.gravatar.com/avatar/${h.md5(item.history.user.email)}?d=iden…"></div> - - ## Page meta. - - ## No links for datasets right now. - - ## Tags. - <p> - <h4>Tags</h4> - <p> - ## Community tags. - <div> - Community: - ${render_community_tagging_element( tagged_item=item, tag_click_fn='community_tag_click', use_toggle_link=False )} - %if len ( item.tags ) == 0: - none - %endif - </div> - ## Individual tags. - <p> - <div> - Yours: - ${render_individual_tagging_element( user=trans.get_user(), tagged_item=item, elt_context='view.mako', use_toggle_link=False, tag_click_fn='community_tag_click' )} - </div> - </div> - </div> - </div> - -</%def> \ No newline at end of file diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/display_application/display.mako --- a/templates/dataset/display_application/display.mako +++ /dev/null @@ -1,12 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%def name="title()">Display Application: ${display_link.link.display_application.name} ${display_link.link.name}</%def> -%for message, status in msg: - ${render_msg( message, status )} -%endfor -%if refresh: -<%def name="metas()"><meta http-equiv="refresh" content="10" /></%def> -<p> -This page will <a href="${trans.request.url}">refresh</a> after 10 seconds. -</p> -%endif diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako +++ /dev/null @@ -1,202 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/message.mako" name="message_ns" import="handle_refresh_frames" /> - -<%def name="title()">${_('Edit Dataset Attributes')}</%def> - -<%def name="stylesheets()"> - ${h.css( "base", "autocomplete_tagging" )} -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${message_ns.handle_refresh_frames()} - ${h.js( "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )} -</%def> - -<%def name="datatype( dataset, datatypes )"> - <select name="datatype"> - %for ext in datatypes: - %if dataset.ext == ext: - <option value="${ext}" selected="yes">${_(ext)}</option> - %else: - <option value="${ext}">${_(ext)}</option> - %endif - %endfor - </select> -</%def> - -%if message: - ${render_msg( message, status )} -%endif - - -<ul class="nav nav-tabs"> - <li class="active"><a href="#attributes" data-toggle="tab">Attributes</a></li> - <li><a href="#convert" data-toggle="tab">Convert Format</a></li> - <li><a href="#datatype" data-toggle="tab">Datatype</a></li> - <li><a href="#permissions" data-toggle="tab">Permissions</a></li> -</ul> - -<div class="tab-content"> - -<div class="tab-pane active toolForm" id="attributes"> - <div class="toolFormTitle">${_('Edit Attributes')}</div> - <div class="toolFormBody"> - <form name="edit_attributes" action="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" method="post"> - <div class="form-row"> - <label> - Name: - </label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${data.get_display_name() | h}" size="40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label> - Info: - </label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <textarea name="info" cols="40" rows="2">${ util.unicodify( data.info ) | h}</textarea> - </div> - <div style="clear: both"></div> - </div> - %if trans.get_user() is not None: - <div class="form-row"> - <label> - Annotation / Notes: - </label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <textarea name="annotation" cols="40" rows="2">${data_annotation | h}</textarea> - </div> - <div style="clear: both"></div> - <div class="toolParamHelp">Add an annotation or notes to a dataset; annotations are available when a history is viewed.</div> - </div> - %endif - %for name, spec in data.metadata.spec.items(): - %if spec.visible: - <div class="form-row"> - <label> - ${spec.desc}: - </label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${data.metadata.get_html_by_name( name, trans=trans )} - </div> - <div style="clear: both"></div> - </div> - %endif - %endfor - <div class="form-row"> - <input type="submit" name="save" value="${_('Save')}"/> - </div> - </form> - <form name="auto_detect" action="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" method="post"> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="submit" name="detect" value="${_('Auto-detect')}"/> - </div> - <div class="toolParamHelp" style="clear: both;"> - This will inspect the dataset and attempt to correct the above column values if they are not accurate. - </div> - </div> - </form> - %if data.missing_meta(): - <div class="form-row"> - <div class="errormessagesmall">${_('Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.')}</div> - </div> - %endif - </div> -</div> - -<div class="tab-pane toolForm" id="convert"> - <div class="toolFormTitle">${_('Convert to new format')}</div> - <div class="toolFormBody"> - <% converters = data.get_converter_types() %> - %if len( converters ) > 0: - <form name="convert_data" action="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" method="post"> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <select name="target_type"> - %for key, value in converters.items(): - <option value="${key}">${value.name}</option> - %endfor - </select> - </div> - <div class="toolParamHelp" style="clear: both;"> - This will create a new dataset with the contents of this dataset converted to a new format. - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="convert_data" value="${_('Convert')}"/> - </div> - </form> - %else: - No conversions available - %endif - </div> -</div> - -<div class="tab-pane toolForm" id="datatype"> - <div class="toolFormTitle">${_('Change data type')}</div> - <div class="toolFormBody"> - %if data.datatype.allow_datatype_change: - <form name="change_datatype" action="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" method="post"> - <div class="form-row"> - <label> - ${_('New Type')}: - </label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${datatype( data, datatypes )} - </div> - <div class="toolParamHelp" style="clear: both;"> - ${_('This will change the datatype of the existing dataset but <i>not</i> modify its contents. Use this if Galaxy has incorrectly guessed the type of your dataset.')} - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="change" value="${_('Save')}"/> - </div> - </form> - %else: - <div class="form-row"> - <div class="warningmessagesmall">${_('Changing the datatype of this dataset is not allowed.')}</div> - </div> - %endif - </div> -</div> -<p /> - -<div class="tab-pane" id="permissions"> -%if trans.app.security_agent.can_manage_dataset( current_user_roles, data.dataset ): - <%namespace file="/dataset/security_common.mako" import="render_permission_form" /> - ${render_permission_form( data.dataset, data.get_display_name(), h.url_for( controller='dataset', action='edit', dataset_id=dataset_id ), all_roles )} -%elif trans.user: - <div class="toolForm"> - <div class="toolFormTitle">View Permissions</div> - <div class="toolFormBody"> - <div class="form-row"> - %if data.dataset.actions: - <ul> - %for action, roles in trans.app.security_agent.get_permissions( data.dataset ).items(): - %if roles: - <li>${action.description}</li> - <ul> - %for role in roles: - <li>${role.name}</li> - %endfor - </ul> - %endif - %endfor - </ul> - %else: - <p>This dataset is accessible by everyone (it is public).</p> - %endif - </div> - </div> - </div> -%else: - Permissions not available (not logged in) -%endif -</div> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/embed.mako --- a/templates/dataset/embed.mako +++ /dev/null @@ -1,19 +0,0 @@ -<%inherit file="/embed_base.mako"/> -<%! - from galaxy.web.framework.helpers import iff -%> - -<%def name="render_item_links( dataset )"> - <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ), to_ext=dataset.ext )}" title="Save dataset" class="icon-button disk tooltip"></a> - ## Links for importing and viewing an item. - <a href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( item.id ) )}" title="Import dataset" class="icon-button import tooltip"></a> - <a class="icon-button go-to-full-screen tooltip" href="${h.url_for( controller='/dataset', action='display_by_username_and_slug', username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) )}" title="Go to dataset"></a> - -</%def> - -<%def name="render_summary_content( dataset, data )"> -## <ul> -## <li>Format : ${dataset.extension} -## <pre>${dataset.peek}</pre> -## </ul> -</%def> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/errors.mako --- a/templates/dataset/errors.mako +++ /dev/null @@ -1,80 +0,0 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> -<html> - <head> - <title>Dataset generation errors</title> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <link href="/static/style/base.css" rel="stylesheet" type="text/css" /> - <style> - pre - { - background: white; - color: black; - border: dotted black 1px; - overflow: auto; - padding: 10px; - } - </style> - </head> - - <body> - <h2>Dataset generation errors</h2> - <p><b>Dataset ${hda.hid}: ${hda.display_name()}</b></p> - <% job = hda.creating_job %> - %if job: - - %if job.traceback: - The Galaxy framework encountered the following error while attempting to run the tool: - <pre>${ util.unicodify( job.traceback ) | h}</pre> - %endif - %if job.stderr or job.info: - Tool execution generated the following error message: - %if job.stderr: - <pre>${ util.unicodify( job.stderr ) | h}</pre> - %elif job.info: - <pre>${ util.unicodify( job.info ) | h}</pre> - %endif - %else: - Tool execution did not generate any error messages. - %endif - %if job.stdout: - The tool produced the following additional output: - <pre>${ util.unicodify( job.stdout ) | h}</pre> - %endif - %else: - The tool did not create any additional job / error info. - %endif - <% - if trans.user: - user_email = trans.user.email - else: - user_email = '' - %> - <h2>Report this error to the Galaxy Team</h2> - <p> - The Galaxy team regularly reviews errors that occur in the application. - However, if you would like to provide additional information (such as - what you were trying to do when the error occurred) and a contact e-mail - address, we will be better able to investigate your problem and get back - to you. - </p> - <div class="toolForm"> - <div class="toolFormTitle">Error Report</div> - <div class="toolFormBody"> - <form name="report_error" action="${h.url_for( action='report_error')}" method="post" > - <input type="hidden" name="id" value="${hda.id}" /> - <div class="form-row"> - <label>Your email</label> - <input type="text" name="email" size="40" value="${user_email}" /> - </div> - <div class="form-row"> - <label>Message</label> - <textarea name="message" rows="10" cols="40"></textarea> - </div> - <div class="form-row"> - <input type="submit" value="Report"/> - </div> - </form> - </div> - </div> - </body> -</html> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/grid.mako --- a/templates/dataset/grid.mako +++ /dev/null @@ -1,1 +0,0 @@ -<%inherit file="/grid_base.mako"/> \ No newline at end of file diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/item_content.mako --- a/templates/dataset/item_content.mako +++ /dev/null @@ -1,3 +0,0 @@ -<%namespace file="/dataset/display.mako" import="*" /> - -${render_item( item, item_data )} \ No newline at end of file diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/large_file.mako --- a/templates/dataset/large_file.mako +++ /dev/null @@ -1,11 +0,0 @@ -<%inherit file="/base.mako"/> - -<div class="warningmessagelarge"> - This dataset is large and only the first megabyte is shown below.<br /> - <a href="${h.url_for( controller='dataset', action='display', dataset_id=trans.security.encode_id( data.id ), filename='' )}">Show all</a> | - <a href="${h.url_for( controller='dataset', action='display', dataset_id=trans.security.encode_id( data.id ), to_ext=data.ext )}">Save</a> -</div> - -<pre> -${ unicode( truncated_data, 'utf-8' ) | h } -</pre> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/security_common.mako --- a/templates/dataset/security_common.mako +++ /dev/null @@ -1,130 +0,0 @@ -<%def name="render_select( current_actions, action_key, action, roles )"> - <% - import sets - in_roles = sets.Set() - for a in current_actions: - if a.action == action.action: - in_roles.add( a.role ) - out_roles = filter( lambda x: x not in in_roles, roles ) - %> - <p> - <b>${action.action}:</b> ${action.description} - %if action == trans.app.security_agent.permitted_actions.DATASET_ACCESS: - <br/> - NOTE: Users must have every role associated with this dataset in order to access it - %endif - </p> - <div style="width: 100%; white-space: nowrap;"> - <div style="float: left; width: 50%;"> - Roles associated:<br /> - <select name="${action_key}_in" id="${action_key}_in_select" class="in_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple> - %for role in in_roles: - <option value="${role.id}">${role.name}</option> - %endfor - </select><br /> - <div style="width: 98%; text-align: right"><input type="submit" id="${action_key}_remove_button" class="role_remove_button" value=">>"/></div> - </div> - <div style="width: 50%;"> - Roles not associated:<br /> - <select name="${action_key}_out" id="${action_key}_out_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple> - %for role in out_roles: - <option value="${role.id}">${role.name}</option> - %endfor - </select><br /> - <input type="submit" id="${action_key}_add_button" class="role_add_button" value="<<"/> - </div> - </div> -</%def> - -## Any permission ( e.g., 'DATASET_ACCESS' ) included in the do_not_render param will not be rendered on the page. -<%def name="render_permission_form( obj, obj_name, form_url, roles, do_not_render=[], all_roles=[] )"> - <% - if isinstance( obj, trans.app.model.User ): - current_actions = obj.default_permissions - permitted_actions = trans.app.model.Dataset.permitted_actions.items() - obj_str = 'user %s' % obj_name - obj_type = 'dataset' - elif isinstance( obj, trans.app.model.History ): - current_actions = obj.default_permissions - permitted_actions = trans.app.model.Dataset.permitted_actions.items() - obj_str = 'history %s' % obj_name - obj_type = 'dataset' - elif isinstance( obj, trans.app.model.Dataset ): - current_actions = obj.actions - permitted_actions = trans.app.model.Dataset.permitted_actions.items() - obj_str = obj_name - obj_type = 'dataset' - elif isinstance( obj, trans.app.model.LibraryDatasetDatasetAssociation ): - current_actions = obj.actions + obj.dataset.actions - permitted_actions = trans.app.model.Dataset.permitted_actions.items() + trans.app.model.Library.permitted_actions.items() - obj_str = obj_name - obj_type = 'dataset' - elif isinstance( obj, trans.app.model.Library ): - current_actions = obj.actions - permitted_actions = trans.app.model.Library.permitted_actions.items() - obj_str = 'library %s' % obj_name - obj_type = 'library' - elif isinstance( obj, trans.app.model.LibraryDataset ): - current_actions = obj.actions - permitted_actions = trans.app.model.Library.permitted_actions.items() - obj_str = 'library dataset %s' % obj_name - obj_type = 'library' - elif isinstance( obj, trans.app.model.LibraryFolder ): - current_actions = obj.actions - permitted_actions = trans.app.model.Library.permitted_actions.items() - obj_str = 'library folder %s' % obj_name - obj_type = 'library' - else: - current_actions = [] - permitted_actions = {}.items() - obj_str = 'unknown object %s' %obj_name - obj_type = '' - %> - <script type="text/javascript"> - $( document ).ready( function () { - $( '.role_add_button' ).click( function() { - var action = this.id.substring( 0, this.id.lastIndexOf( '_add_button' ) ) - var in_select = '#' + action + '_in_select'; - var out_select = '#' + action + '_out_select'; - return !$( out_select + ' option:selected' ).remove().appendTo( in_select ); - }); - $( '.role_remove_button' ).click( function() { - var action = this.id.substring( 0, this.id.lastIndexOf( '_remove_button' ) ) - var in_select = '#' + action + '_in_select'; - var out_select = '#' + action + '_out_select'; - return !$( in_select + ' option:selected' ).remove().appendTo( out_select ); - }); - $( 'form#edit_role_associations' ).submit( function() { - $( '.in_select option' ).each(function( i ) { - $( this ).attr( "selected", "selected" ); - }); - }); - }); - </script> - <div class="toolForm"> - <div class="toolFormTitle">Manage ${obj_type} permissions on ${obj_str}</div> - <div class="toolFormBody"> - <form name="edit_role_associations" id="edit_role_associations" action="${form_url}" method="post"> - <div class="form-row"></div> - %for k, v in permitted_actions: - %if k not in do_not_render: - <div class="form-row"> - ## LIBRARY_ACCESS is a special case because we need to render all roles instead of - ## roles derived from the roles associated with LIBRARY_ACCESS. - <% render_all_roles = k == 'LIBRARY_ACCESS' %> - %if render_all_roles: - ${render_select( current_actions, k, v, all_roles )} - %else: - ${render_select( current_actions, k, v, roles )} - %endif - </div> - %endif - %endfor - <div class="form-row"> - <input type="submit" name="update_roles_button" value="Save"/> - </div> - </form> - </div> - </div> - <p/> -</%def> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/tabular_chunked.mako --- a/templates/dataset/tabular_chunked.mako +++ /dev/null @@ -1,103 +0,0 @@ -<%inherit file="/base.mako"/> - - -<%def name="title()">Dataset Display</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - var DATASET_URL = "${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ))}"; - var COLUMN_NUMBER = ${column_number}; - var COLUMN_TYPES = ${column_types}; - var COLUMN_NAMES = ${column_names}; - - var chunk = ${chunk}; - var current_chunk = 0; - - function renderCell(cell_contents, index, colspan){ - if (colspan !== undefined){ - return $('<td>').attr('colspan', colspan).addClass('stringalign').text(cell_contents); - } - else if (COLUMN_TYPES[index] == 'str' || COLUMN_TYPES[index] == 'list'){ - /* Left align all str columns, right align the rest */ - return $('<td>').addClass('stringalign').text(cell_contents);; - } - else{ - return $('<td>').text(cell_contents); - } - } - - function renderRow(line){ - /* Check length of cells to ensure this is a complete row. */ - var cells = line.split('\t'); - var row = $('<tr>'); - if (cells.length == COLUMN_NUMBER){ - $.each(cells, function(index, cell_contents){ - row.append(renderCell(cell_contents, index)); - }); - } - else if(cells.length > COLUMN_NUMBER){ - /* SAM file or like format with optional metadata included */ - $.each(cells.slice(0, COLUMN_NUMBER -1), function(index, cell_contents){ - row.append(renderCell(cell_contents, index)); - }); - row.append(renderCell(cells.slice(COLUMN_NUMBER -1).join('\t'), COLUMN_NUMBER-1)); - } - else if(COLUMN_NUMBER > 5 && cells.length == COLUMN_NUMBER - 1 ){ - /* SAM file or like format with optional metadata missing */ - $.each(cells, function(index, cell_contents){ - row.append(renderCell(cell_contents, index)); - }); - row.append($('<td>')); - } - else{ - /* Comment line, just return the one cell*/ - row.append(renderCell(line, 0, COLUMN_NUMBER)); - } - return row; - } - - function renderChunk(chunk){ - var table = $('#content_table'); - if (chunk.ck_data == ""){ - current_chunk = -1; - } - else if(chunk.ck_index === current_chunk + 1){ - if (current_chunk === 0 && COLUMN_NAMES){ - table.append('<tr><th>' + COLUMN_NAMES.join('</th><th>') + '</th></tr>'); - } - var lines = chunk.ck_data.split('\n'); - $.each(lines, function(index, line){ - table.append(renderRow(line)); - }); - current_chunk = chunk.ck_index; - } - } - - $(document).ready(function(){ - renderChunk(chunk); - $(window).scroll(function(){ - if ($(window).scrollTop() == $(document).height() - $(window).height()){ - if (current_chunk !== -1){ - $.getJSON(DATASET_URL, - {chunk: current_chunk}, - function(result){renderChunk(result)}); - } - } - }); - $('#loading_indicator').ajaxStart(function(){ - $(this).show(); - }).ajaxStop(function(){ - $(this).hide(); - }); - }); - </script> -</%def> - -<%def name="stylesheets()"> - ${parent.stylesheets()} -</%def> - -<div id="loading_indicator" ></div> -<table id="content_table" cellpadding="0"> -</table> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/copy.mako --- a/templates/history/copy.mako +++ /dev/null @@ -1,27 +0,0 @@ -<% _=n_ %> -<%inherit file="/base.mako"/> -<%def name="title()">Copy History</%def> - -<div class="toolForm"> - <div class="toolFormTitle">Copy History</div> - <div class="toolFormBody"> - <form action="${h.url_for( controller='history', action='copy' )}" method="post" > - <div class="form-row"> - %if id_argument is not None: - <input type="hidden" name="id" value="${id_argument}"> - %endif - You can make a copy of the history that includes all datasets in the original history or just the active - (not deleted) datasets. - </div> - <div class="form-row"> - <input type="radio" name="copy_choice" value="activatable"> Copy all datasets, including deleted ones - </div> - <div class="form-row"> - <input type="radio" name="copy_choice" value="active"> Copy only active (not deleted) datasets - </div> - <div class="form-row"> - <input type="submit" name="copy_choice_button" value="Copy"> - </div> - </form> - </div> -</div> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/display.mako --- a/templates/history/display.mako +++ /dev/null @@ -1,84 +0,0 @@ -<%inherit file="/display_base.mako"/> -<%namespace file="/root/history_common.mako" import="render_dataset" /> - -## Set vars so that there's no need to change the code below. -<% - history = published_item - datasets = published_item_data -%> - -<%def name="javascripts()"> - ${parent.javascripts()} -</%def> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "history" )} - <style type="text/css"> - .historyItemBody { - display: none; - } - .column { - float: left; - padding: 10px; - margin: 20px; - background: #666; - border: 5px solid #ccc; - width: 300px; - } - </style> - - <noscript> - <style> - .historyItemBody { - display: block; - } - </style> - </noscript> -</%def> - -<%def name="render_item_links( history )"> - <a - href="${h.url_for( controller='/history', action='imp', id=trans.security.encode_id(history.id) )}" - class="icon-button import" - ## Needed to overwide initial width so that link is floated left appropriately. - style="width: 100%" - title="Import history">Import history</a> -</%def> - -<%def name="render_item( history, datasets )"> - %if history.deleted: - <div class="warningmessagesmall"> - ${_('You are currently viewing a deleted history!')} - </div> - <p></p> - %endif - - %if not datasets: - <div class="infomessagesmall" id="emptyHistoryMessage"> - %else: - ## Render requested datasets, ordered from newest to oldest, including annotations. - <table class="annotated-item"> - <tr><th>Dataset</th><th class="annotation">Annotation</th></tr> - %for data in datasets: - <tr> - %if data.visible: - <td> - <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )} - </div> - </td> - <td class="annotation"> - %if hasattr( data, "annotation") and data.annotation is not None: - ${data.annotation} - %endif - </td> - %endif - </tr> - %endfor - </table> - <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> - %endif - ${_("This history is empty.")} - </div> -</%def> \ No newline at end of file diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/display_structured.mako --- a/templates/history/display_structured.mako +++ /dev/null @@ -1,132 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/root/history_common.mako" import="render_dataset" /> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "history" )} - <style type="text/css"> - body { - background: white; - padding: 5px; - } - - .clickable { - cursor: pointer; - } - - .workflow { - border: solid gray 1px; - margin: 5px 0; - border-left-width: 5px; - } - - .workflow > .header { - background: lightgray; - padding: 5px 10px; - - font-weight: bold; - } - - .workflow > .body { - border-top: solid gray 1px; - padding: 5px; - } - - div.toolForm { - margin: 5px 0; - border-left-width: 5px; - } - div.toolFormBody { - padding: 5px 5px; - } - </style> -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - $(function(){ - - $(".workflow, .tool").each( function() { - var body = $(this).children( ".body" ); - $(this).children( ".header" ).click( function() { - body.toggle(); - }).addClass( "clickable" ); - // body.hide(); - }); - - $(".historyItem").each( function() { - var id = this.id; - var body = $(this).children( "div.historyItemBody" ); - var peek = body.find( "pre.peek" ) - $(this).children( ".historyItemTitleBar" ).find( ".historyItemTitle" ).wrap( "<a href='#'></a>" ).click( function() { - if ( body.is(":visible") ) { - // Hiding stuff here - if ( $.browser.mozilla ) { peek.css( "overflow", "hidden" ) } - body.slideUp( "fast" ); - } else { - // Showing stuff here - body.slideDown( "fast", function() { - if ( $.browser.mozilla ) { peek.css( "overflow", "auto" ); } - }); - } - return false; - }); - body.hide(); - }); - }); - </script> -</%def> - -<%def name="render_item( entity, children )"> -<% -entity_name = entity.__class__.__name__ -if entity_name == "HistoryDatasetAssociation": - render_item_hda( entity, children ) -elif entity_name == "Job": - render_item_job( entity, children ) -elif entity_name == "WorkflowInvocation": - render_item_wf( entity, children ) -%> -</%def> - -<%def name="render_item_hda( hda, children )"> - ${render_dataset( hda, hda.hid, display_structured=True )} -</%def> - -<%def name="render_item_job( job, children )"> - - <div class="tool toolForm"> - <% - tool = trans.app.toolbox.get_tool( job.tool_id ) - if tool: - tool_name = tool.name - else: - tool_name = "Unknown tool with id '%s'" % job.tool_id - %> - <div class="header toolFormTitle">Tool: ${tool_name}</div> - <div class="body toolFormBody"> - %for e, c in reversed( children ): - ${render_item( e, c )} - %endfor - </div> - </div> - -</%def> - -<%def name="render_item_wf( wf, children )"> - - <div class="workflow"> - <div class="header">Workflow: ${wf.workflow.name}</div> - <div class="body"> - %for e, c in reversed( children ): - ${render_item( e, c )} - %endfor - </div> - </div> - -</%def> - -%for entity, children in items: - ${render_item( entity, children )} -%endfor \ No newline at end of file diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/embed.mako --- a/templates/history/embed.mako +++ /dev/null @@ -1,13 +0,0 @@ -<%inherit file="/embed_base.mako"/> -<%! - from galaxy.web.framework.helpers import iff -%> - -<%def name="render_summary_content( history, datasets )"> - -## <ul> -## <% num_datasets = len ( datasets ) %> -## <li>${num_datasets} dataset${iff( num_datasets != 1, "s", "" )} -## <li>Operations: ... -## </ul> -</%def> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/grid.mako --- a/templates/history/grid.mako +++ /dev/null @@ -1,25 +0,0 @@ -<%inherit file="../grid_base.mako"/> - -<%def name="grid_javascripts()"> - ${parent.grid_javascripts()} - <script type="text/javascript"> - %if refresh_frames: - %if 'history' in refresh_frames: - if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; - if ( parent.force_right_panel ) { - parent.force_right_panel( 'show' ); - } - } - %endif - %endif - </script> -</%def> - -<%def name="grid_body( grid )"> - ${self.make_grid( grid )} - <br/> - <div class="toolParamHelp" style="clear: both;"> - Histories that have been deleted for more than a time period specified by the Galaxy administrator(s) may be permanently deleted. - </div> -</%def> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/item_content.mako --- a/templates/history/item_content.mako +++ /dev/null @@ -1,3 +0,0 @@ -<%namespace file="/history/display.mako" import="*" /> - -${render_item( item, item_data )} \ No newline at end of file diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/list_as_xml.mako --- a/templates/history/list_as_xml.mako +++ /dev/null @@ -1,7 +0,0 @@ -<?xml version="1.0"?> -<history_ids> - %for i, history in enumerate( t.user.histories ): - <data id="${trans.security.encode_id( history.id )}" hid="${i+1}" num="${len(history.datasets)}" name="${history.name}" create="${history.create_time}" update="${history.update_time}" > - </data> - %endfor -</history_ids> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/list_published.mako --- a/templates/history/list_published.mako +++ /dev/null @@ -1,34 +0,0 @@ -<%inherit file="/webapps/galaxy/base_panels.mako"/> - -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=False - self.active_view="shared" - self.message_box_visible=False -%> -</%def> - -<%def name="title()"> - Galaxy | Published Histories -</%def> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - <style> - .grid td { - min-width: 100px; - } - </style> -</%def> - -<%def name="center_panel()"> - - <div style="overflow: auto; height: 100%;"> - <div class="page-container" style="padding: 10px;"> - ${h.to_unicode( grid )} - </div> - </div> - - -</%def> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/options.mako --- a/templates/history/options.mako +++ /dev/null @@ -1,32 +0,0 @@ -<% _=n_ %> -<%inherit file="/base.mako"/> -<%def name="title()">History options</%def> - -<h2>${_('History Options')}</h2> - -%if not user: -<div class="infomessage"> - <div>${_('You must be ')}<a target="galaxy_main" href="${h.url_for( controller='user', action='login' )}">${_('logged in')}</a>${_(' to store or switch histories.')}</div> -</div> -%endif - -<ul> - %if user: - <li><a href="${h.url_for( controller='history', action='list')}" target="galaxy_main">Previously</a> stored histories</li> - %if len( history.active_datasets ) > 0: - <li><a href="${h.url_for( controller='root', action='history_new' )}">Create</a> a new empty history</li> - <li><a href="${h.url_for( controller='workflow', action='build_from_current_history' )}">Construct workflow</a> from current history</li> - <li><a href="${h.url_for( controller='history', action='copy', id=trans.security.encode_id( history.id ) )}">Copy</a> current history</li> - %endif - <li><a href="${h.url_for( controller='history', action='share' )}" target="galaxy_main">Share</a> current history</div> - <li><a href="${h.url_for( controller='root', action='history_set_default_permissions' )}">Change default permissions</a> for current history</li> - %endif - %if len( history.activatable_datasets ) > 0: - <li><a href="${h.url_for( controller='root', action='history', show_deleted=True)}" target="galaxy_history">Show deleted</a> datasets in current history</li> - %endif - <li><a href="${h.url_for( controller='history', action='rename', id=trans.security.encode_id( history.id ) )}" target="galaxy_main">Rename</a> current history (stored as "${history.name}")</li> - <li><a href="${h.url_for( controller='history', action='delete_current' )}" confirm="Are you sure you want to delete the current history?">Delete</a> current history</div> - %if user and user.histories_shared_by_others: - <li><a href="${h.url_for( controller='history', action='list_shared')}" target="galaxy_main">Histories</a> shared with you by others</li> - %endif -</ul> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/permissions.mako --- a/templates/history/permissions.mako +++ /dev/null @@ -1,8 +0,0 @@ -<%inherit file="/base.mako"/> -<%def name="title()">Change Default Permissions on New Datasets in This History</%def> -<%namespace file="/dataset/security_common.mako" import="render_permission_form" /> - -%if trans.user: - <% history = trans.get_history() %> - ${render_permission_form( history, history.name, h.url_for(), trans.user.all_roles() )} -%endif diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/rename.mako --- a/templates/history/rename.mako +++ /dev/null @@ -1,38 +0,0 @@ -<%inherit file="/base.mako"/> -<%def name="title()">${_('Rename History')}</%def> - -<div class="toolForm"> - <div class="toolFormTitle">${_('Rename')}</div> - <div class="toolFormBody"> - <form action="${h.url_for( controller='history', action='rename' )}" method="post" > - <div class="form-row"> - <table> - <thead> - <tr> - <th>${_('Current Name')}</th> - <th>${_('New Name')}</th> - </tr> - </thead> - <tbody> - %for history in histories: - <tr> - <td> - <input type="hidden" name="id" value="${trans.security.encode_id( history.id )}"> - ${history.get_display_name() | h} - </td> - <td> - <input type="text" name="name" value="${history.get_display_name() | h}" size="40"> - </td> - </tr> - %endfor - </tbody> - <tr> - <td colspan="2"> - <input type="submit" name="history_rename_btn" value="${_('Rename Histories')}"> - </td> - </tr> - </table> - </div> - </form> - </div> -</div> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/share.mako --- a/templates/history/share.mako +++ /dev/null @@ -1,192 +0,0 @@ -<% _=n_ %> -<%inherit file="/base.mako"/> -<%def name="title()">Share histories</%def> - -<div class="toolForm"> - <div class="toolFormTitle">Share ${len( histories)} histories</div> - <div class="toolFormBody"> - %if not can_change and not cannot_change and not no_change_needed: - ## We are sharing histories that contain only public datasets - <form name='share' id='share' action="${h.url_for( action='share' )}" method="post" > - <div class="form-title-row"><b>Histories to be shared:</b></div> - <div class="form-row" style="padding-left: 2em;"> - <table width="100%"> - <thead> - <th>${_('History Name')}</th> - <th>${_('Number of Datasets')}</th> - </thead> - <tbody> - %for history in histories: - <tr> - <td> - <input type="hidden" name="id" value="${trans.security.encode_id( history.id )}"> - ${ util.unicodify( history.name )} - </td> - <td> - %if len( history.datasets ) < 1: - <div class="warningmark">${_('This history contains no data.')}</div> - %else: - ${len(history.datasets)} - %endif - </td> - </tr> - %endfor - </tbody> - </table> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <label>Galaxy user emails with which to share histories</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="email" value="${email}" size="40"> - </div> - <div class="toolParamHelp" style="clear: both;"> - Enter a Galaxy user email address or a comma-separated list of addresses if sharing with multiple users - </div> - </div> - %if send_to_err: - <div style="clear: both"></div> - <div class="form-row"> - <div class="errormessage">${send_to_err}</div> - </div> - %endif - <div style="clear: both"></div> - <div class="form-row"> - <input type="submit" name="share_button" value="Submit"> - </div> - </form> - %else: - ## We are sharing restricted histories - %if no_change_needed or can_change: - <form name='share_restricted' id=share_restricted' action="${h.url_for( controller='history', action='share_restricted' )}" method="post"> - %if send_to_err: - <div style="clear: both"></div> - <div class="form-row"> - <div class="errormessage">${send_to_err}</div> - </div> - %endif - ## Needed for rebuilding dicts - <input type="hidden" name="email" value="${email}" size="40"> - %for history in histories: - <input type="hidden" name="id" value="${trans.security.encode_id( history.id )}"> - %endfor - %if no_change_needed: - ## no_change_needed looks like: {historyX : [hda, hda], historyY : [hda] } - <div style="clear: both"></div> - <div class="form-row"> - <div class="donemessage"> - The following datasets can be shared with ${email} with no changes - </div> - </div> - %for history, hdas in no_change_needed.items(): - <div class="form-row"> - <label>History</label> - ${util.unicodify( history.name )} - </div> - <div style="clear: both"></div> - <div class="form-row"> - <label>Datasets</label> - </div> - %for hda in hdas: - <div class="form-row"> - ${util.unicodify( hda.name )} - %if hda.deleted: - (deleted) - %endif - </div> - %endfor - %endfor - %endif - %if can_change: - ## can_change looks like: {historyX : [hda, hda], historyY : [hda] } - <div style="clear: both"></div> - <div class="form-row"> - <div class="warningmessage"> - The following datasets can be shared with ${email} by updating their permissions - </div> - </div> - %for history, hdas in can_change.items(): - <div class="form-row"> - <label>History</label> - ${util.unicodify( history.name )} - </div> - <div style="clear: both"></div> - <div class="form-row"> - <label>Datasets</label> - </div> - %for hda in hdas: - <div class="form-row"> - ${util.unicodify( hda.name )} - %if hda.deleted: - (deleted) - %endif - </div> - %endfor - %endfor - %endif - %if cannot_change: - ## cannot_change looks like: {historyX : [hda, hda], historyY : [hda] } - <div style="clear: both"></div> - <div class="form-row"> - <div class="errormessage"> - The following datasets cannot be shared with ${email} because you are not authorized to - change the permissions on them - </div> - </div> - %for history, hdas in cannot_change.items(): - <div class="form-row"> - <label>History</label> - ${util.unicodify( history.name )} - </div> - <div style="clear: both"></div> - <div class="form-row"> - <label>Datasets</label> - </div> - %for hda in hdas: - <div class="form-row"> - ${util.unicodify( hda.name )} - %if hda.deleted: - (deleted) - %endif - </div> - %endfor - %endfor - %endif - <div class="toolFormTitle"></div> - <div class="form-row"> - <label>How would you like to proceed?</label> - </div> - %if can_change: - <div class="form-row"> - <input type="radio" name="action" value="public"> Make datasets public so anyone can access them - %if cannot_change: - (where possible) - %endif - </div> - <div class="form-row"> - %if no_change_needed: - <input type="radio" name="action" value="private"> Make datasets private to me and the user(s) with whom I am sharing - %else: - <input type="radio" name="action" value="private" checked> Make datasets private to me and the user(s) with whom I am sharing - %endif - %if cannot_change: - (where possible) - %endif - </div> - %endif - %if no_change_needed: - <div class="form-row"> - <input type="radio" name="action" value="share_anyway" checked> Share anyway - %if can_change: - (don't change any permissions) - %endif - </div> - %endif - <div class="form-row"> - <input type="submit" name="share_restricted_button" value="Go"><br/> - </div> - </form> - %endif - %endif - </div> -</div> diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/view.mako --- a/templates/history/view.mako +++ /dev/null @@ -1,140 +0,0 @@ -<%namespace file="/display_common.mako" import="get_history_link, get_controller_name" /> -<%namespace file="/root/history_common.mako" import="render_dataset" /> -<%namespace file="/tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" /> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/galaxy/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js( "libs/jquery/jstorage" )} - <script type="text/javascript"> - $(function() { - init_history_items( $("div.historyItemWrapper"), false, "nochanges" ); - }); - </script> -</%def> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "history", "autocomplete_tagging" )} - <style type="text/css"> - .historyItemContainer { - padding-right: 3px; - border-right-style: solid; - border-right-color: #66AA66; - } - .page-body - { - padding: 10px; - float: left; - width: 65%; - } - .page-meta - { - float: right; - width: 27%; - padding: 0.5em; - margin: 0.25em; - vertical-align: text-top; - border: 2px solid #DDDDDD; - border-top: 4px solid #DDDDDD; - } - </style> - - <style> - .historyItemBody { - display: none; - } - </style> - - <noscript> - <style> - .historyItemBody { - display: block; - } - </style> - </noscript> -</%def> - -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=False - self.message_box_visible=False -%> -</%def> - -<%def name="body()"> - ${center_panel()} -</%def> - -<%def name="center_panel()"> - ## Get URL to other histories owned by user that owns this history. - <% - ##TODO: is there a better way to create this URL? Can't use 'f-username' as a key b/c it's not a valid identifier. - href_to_published_histories = h.url_for( controller='/history', action='list_published') - if history.user is not None: - href_to_user_histories = h.url_for( controller='/history', action='list_published', xxx=history.user.username).replace( 'xxx', 'f-username') - else: - href_to_user_histories = h.url_for( controller='/history', action='list_published' )##should this instead be be None or empty string? - %> - - <div class="unified-panel-header" unselectable="on"> - </div> - - <div class="unified-panel-body"> - <div style="overflow: auto; height: 100%;"> - ## Render view of history. - <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px"> - %if not history.purged: - <a href="${h.url_for( action='imp', id=trans.security.encode_id(history.id) )}">import and start using history</a> | - <a href="${get_history_link( history )}">${_('refresh')}</a> | - %endif - %if show_deleted: - <a href="${h.url_for( id=trans.security.encode_id(history.id), show_deleted=False, use_panels=use_panels )}">${_('hide deleted')}</a> | - %else: - <a href="${h.url_for( id=trans.security.encode_id(history.id), show_deleted=True, use_panels=use_panels )}">${_('show deleted')}</a> | - %endif - <a href="#" class="toggle">collapse all</a> - </div> - - <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px"> - <div id="history-name">${history.get_display_name()}</div> - </div> - - %if history.deleted: - <div class="warningmessagesmall"> - ${_('You are currently viewing a deleted history!')} - </div> - <p></p> - %endif - - %if not datasets: - - <div class="infomessagesmall" id="emptyHistoryMessage"> - - %else: - - ## Render requested datasets, ordered from newest to oldest - %for data in datasets: - %if data.visible: - <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )} - </div> - %endif - %endfor - - <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> - %endif - ${_("Your history is empty. Click 'Get Data' on the left pane to start")} - </div> - </div> - </div> -</%def> This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: james_taylor: base_panels: no longer need to specify has_(left|right)_panel, determined depending on whether the blocks are set. Moved some CSS into base.css
by Bitbucket 03 Feb '13

03 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c714feaad115/ changeset: c714feaad115 user: james_taylor date: 2013-02-04 04:57:32 summary: base_panels: no longer need to specify has_(left|right)_panel, determined depending on whether the blocks are set. Moved some CSS into base.css affected #: 6 files diff -r d2b192832826f531e7702461826822dbb8179acb -r c714feaad11541377edd84af1179869c1a8e4f47 lib/galaxy/webapps/galaxy/controllers/library.py --- a/lib/galaxy/webapps/galaxy/controllers/library.py +++ b/lib/galaxy/webapps/galaxy/controllers/library.py @@ -79,6 +79,7 @@ default_action=default_action, message=message, status=status ) + @web.expose def browse_libraries( self, trans, **kwd ): if 'operation' in kwd: diff -r d2b192832826f531e7702461826822dbb8179acb -r c714feaad11541377edd84af1179869c1a8e4f47 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -31,8 +31,19 @@ background-repeat: repeat-x; background-position: top; margin: 10px; + + // For panel layout pages + &.full-content { + overflow: hidden; + margin: 0; + padding: 0; + width: 100%; + height: 100%; + } + } + img { border: 0; } @@ -410,7 +421,7 @@ width:100%; min-width:900px; height:32px; - // background: @masthead_bg; + background: @masthead_bg; // color:#fff; border-bottom: solid @layout_masthead_border 1px; z-index: 15000; diff -r d2b192832826f531e7702461826822dbb8179acb -r c714feaad11541377edd84af1179869c1a8e4f47 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -892,7 +892,7 @@ .clear:after{clear:both;} .clear:before,.clear:after{display:table;content:"";line-height:0;} .clear:after{clear:both;} -body{background:#ffffff;color:#303030;background-image:url(base_bg.png);background-repeat:repeat-x;background-position:top;margin:10px;} +body{background:#ffffff;color:#303030;background-image:url(base_bg.png);background-repeat:repeat-x;background-position:top;margin:10px;}body.full-content{overflow:hidden;margin:0;padding:0;width:100%;height:100%;} img{border:0;} a,a:link,a:visited,a:active{text-decoration:underline;color:#303030;} .nav-tabs a{text-decoration:none;} @@ -936,7 +936,7 @@ .panel-warning-message{background-image:url(warn_small.png);background-color:#ffffcc;} .panel-done-message{background-image:url(ok_small.png);background-color:#ccffcc;} .panel-info-message{background-image:url(info_small.png);background-color:#d9edf7;} -#masthead{-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;overflow:visible;margin-bottom:16px;*position:relative;*z-index:2;position:absolute;top:0;left:0;width:100%;min-width:900px;height:32px;border-bottom:solid #444444 1px;z-index:15000;padding:0;}#masthead .nav{z-index:10000;background-color:#2c3143;} +#masthead{-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;overflow:visible;margin-bottom:16px;*position:relative;*z-index:2;position:absolute;top:0;left:0;width:100%;min-width:900px;height:32px;background:#2c3143;border-bottom:solid #444444 1px;z-index:15000;padding:0;}#masthead .nav{z-index:10000;background-color:#2c3143;} #masthead .nav>li>a{padding:8px 10px 8px;cursor:pointer;}#masthead .nav>li>a:hover{color:gold;} #masthead .dropdown-menu a,#masthead .dropdown-menu a:hover{text-decoration:none;} #masthead .dropdown-toggle .caret{margin-top:7px;} diff -r d2b192832826f531e7702461826822dbb8179acb -r c714feaad11541377edd84af1179869c1a8e4f47 static/june_2007_style/galaxy_bootstrap.less --- a/static/june_2007_style/galaxy_bootstrap.less +++ b/static/june_2007_style/galaxy_bootstrap.less @@ -107,7 +107,6 @@ margin-left: -330px; } - .modal:after { content: ""; height: 0px; @@ -115,8 +114,7 @@ top: 50px; display: block; border: solid transparent 1px; -}; - +} .modal-body { height: auto; @@ -203,4 +201,4 @@ border-width: 0 @tooltipArrowWidth @tooltipArrowWidth; border-bottom-color: @tooltipArrowColor; } -} \ No newline at end of file +} diff -r d2b192832826f531e7702461826822dbb8179acb -r c714feaad11541377edd84af1179869c1a8e4f47 templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -1,8 +1,8 @@ <!DOCTYPE HTML><% - self.has_left_panel=True - self.has_right_panel=True + self.has_left_panel = hasattr( self, 'left_panel' ) + self.has_right_panel = hasattr( self, 'right_panel' ) self.message_box_visible=False self.overlay_visible=False self.message_box_class="" @@ -17,15 +17,8 @@ ## Default stylesheets <%def name="stylesheets()"> - ${h.css('base','panel_layout','jquery.rating')} + ${h.css('base','jquery.rating')} <style type="text/css"> - body, html { - overflow: hidden; - margin: 0; - padding: 0; - width: 100%; - height: 100%; - } #center { %if not self.has_left_panel: left: 0 !important; @@ -270,7 +263,7 @@ ${self.javascripts()} </head> - <body scroll="no" class="${self.body_class}"> + <body scroll="no" class="full-content ${self.body_class}"> %if self.require_javascript: <noscript><div class="overlay overlay-background"> diff -r d2b192832826f531e7702461826822dbb8179acb -r c714feaad11541377edd84af1179869c1a8e4f47 templates/workflow/index.mako --- a/templates/workflow/index.mako +++ b/templates/workflow/index.mako @@ -2,10 +2,7 @@ <%def name="init()"><% - self.has_left_panel=False - self.has_right_panel=False self.active_view="workflow" - self.message_box_visible=False %></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: james_taylor: Customize errormiddleware with a better appearence for internal server errors, show sentry ID is enabled, modify sentry middleware to store id in environment and pass request_id with log messages
by Bitbucket 02 Feb '13

02 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d2b192832826/ changeset: d2b192832826 user: james_taylor date: 2013-02-03 01:39:42 summary: Customize errormiddleware with a better appearence for internal server errors, show sentry ID is enabled, modify sentry middleware to store id in environment and pass request_id with log messages affected #: 3 files diff -r fc99a36f9d2195bc742f6e557ae56b7b61ad6766 -r d2b192832826f531e7702461826822dbb8179acb lib/galaxy/web/framework/middleware/error.py --- /dev/null +++ b/lib/galaxy/web/framework/middleware/error.py @@ -0,0 +1,484 @@ +# Like many things, this started life as part of Paste + +# (c) 2005 Ian Bicking and contributors; written for Paste (http://pythonpaste.org) +# Licensed under the MIT license: http://www.opensource.org/licenses/mit-license.php + +""" +Error handler middleware + +When an exception is thrown from the wrapper application, this logs +the exception and displays an error page. +""" +import sys +import traceback +import cgi +try: + from cStringIO import StringIO +except ImportError: + from StringIO import StringIO +from paste.exceptions import formatter, collector, reporter +from paste import wsgilib +from paste import request + +__all__ = ['ErrorMiddleware', 'handle_exception'] + +class _NoDefault(object): + def __repr__(self): + return '<NoDefault>' +NoDefault = _NoDefault() + +class ErrorMiddleware(object): + + """ + Error handling middleware + + Usage:: + + error_catching_wsgi_app = ErrorMiddleware(wsgi_app) + + Settings: + + ``debug``: + If true, then tracebacks will be shown in the browser. + + ``error_email``: + an email address (or list of addresses) to send exception + reports to + + ``error_log``: + a filename to append tracebacks to + + ``show_exceptions_in_wsgi_errors``: + If true, then errors will be printed to ``wsgi.errors`` + (frequently a server error log, or stderr). + + ``from_address``, ``smtp_server``, ``error_subject_prefix``, ``smtp_username``, ``smtp_password``, ``smtp_use_tls``: + variables to control the emailed exception reports + + ``error_message``: + When debug mode is off, the error message to show to users. + + ``xmlhttp_key``: + When this key (default ``_``) is in the request GET variables + (not POST!), expect that this is an XMLHttpRequest, and the + response should be more minimal; it should not be a complete + HTML page. + + Environment Configuration: + + ``paste.throw_errors``: + If this setting in the request environment is true, then this + middleware is disabled. This can be useful in a testing situation + where you don't want errors to be caught and transformed. + + ``paste.expected_exceptions``: + When this middleware encounters an exception listed in this + environment variable and when the ``start_response`` has not + yet occurred, the exception will be re-raised instead of being + caught. This should generally be set by middleware that may + (but probably shouldn't be) installed above this middleware, + and wants to get certain exceptions. Exceptions raised after + ``start_response`` have been called are always caught since + by definition they are no longer expected. + + """ + + def __init__(self, application, global_conf=None, + debug=NoDefault, + error_email=None, + error_log=None, + show_exceptions_in_wsgi_errors=NoDefault, + from_address=None, + smtp_server=None, + smtp_username=None, + smtp_password=None, + smtp_use_tls=False, + error_subject_prefix=None, + error_message=None, + xmlhttp_key=None): + from paste.util import converters + self.application = application + # @@: global_conf should be handled elsewhere in a separate + # function for the entry point + if global_conf is None: + global_conf = {} + if debug is NoDefault: + debug = converters.asbool(global_conf.get('debug')) + if show_exceptions_in_wsgi_errors is NoDefault: + show_exceptions_in_wsgi_errors = converters.asbool(global_conf.get('show_exceptions_in_wsgi_errors')) + self.debug_mode = converters.asbool(debug) + if error_email is None: + error_email = (global_conf.get('error_email') + or global_conf.get('admin_email') + or global_conf.get('webmaster_email') + or global_conf.get('sysadmin_email')) + self.error_email = converters.aslist(error_email) + self.error_log = error_log + self.show_exceptions_in_wsgi_errors = show_exceptions_in_wsgi_errors + if from_address is None: + from_address = global_conf.get('error_from_address', 'errors@localhost') + self.from_address = from_address + if smtp_server is None: + smtp_server = global_conf.get('smtp_server', 'localhost') + self.smtp_server = smtp_server + self.smtp_username = smtp_username or global_conf.get('smtp_username') + self.smtp_password = smtp_password or global_conf.get('smtp_password') + self.smtp_use_tls = smtp_use_tls or converters.asbool(global_conf.get('smtp_use_tls')) + self.error_subject_prefix = error_subject_prefix or '' + if error_message is None: + error_message = global_conf.get('error_message') + self.error_message = error_message + if xmlhttp_key is None: + xmlhttp_key = global_conf.get('xmlhttp_key', '_') + self.xmlhttp_key = xmlhttp_key + + def __call__(self, environ, start_response): + """ + The WSGI application interface. + """ + # We want to be careful about not sending headers twice, + # and the content type that the app has committed to (if there + # is an exception in the iterator body of the response) + if environ.get('paste.throw_errors'): + return self.application(environ, start_response) + environ['paste.throw_errors'] = True + + try: + __traceback_supplement__ = Supplement, self, environ + sr_checker = ResponseStartChecker(start_response) + app_iter = self.application(environ, sr_checker) + return self.make_catching_iter(app_iter, environ, sr_checker) + except: + exc_info = sys.exc_info() + try: + for expect in environ.get('paste.expected_exceptions', []): + if isinstance(exc_info[1], expect): + raise + start_response('500 Internal Server Error', + [('content-type', 'text/html')], + exc_info) + # @@: it would be nice to deal with bad content types here + response = self.exception_handler(exc_info, environ) + return [response] + finally: + # clean up locals... + exc_info = None + + def make_catching_iter(self, app_iter, environ, sr_checker): + if isinstance(app_iter, (list, tuple)): + # These don't raise + return app_iter + return CatchingIter(app_iter, environ, sr_checker, self) + + def exception_handler(self, exc_info, environ): + simple_html_error = False + if self.xmlhttp_key: + get_vars = wsgilib.parse_querystring(environ) + if dict(get_vars).get(self.xmlhttp_key): + simple_html_error = True + return handle_exception( + exc_info, environ['wsgi.errors'], + html=True, + debug_mode=self.debug_mode, + error_email=self.error_email, + error_log=self.error_log, + show_exceptions_in_wsgi_errors=self.show_exceptions_in_wsgi_errors, + error_email_from=self.from_address, + smtp_server=self.smtp_server, + smtp_username=self.smtp_username, + smtp_password=self.smtp_password, + smtp_use_tls=self.smtp_use_tls, + error_subject_prefix=self.error_subject_prefix, + error_message=self.error_message, + simple_html_error=simple_html_error, + environ=environ) + +class ResponseStartChecker(object): + def __init__(self, start_response): + self.start_response = start_response + self.response_started = False + + def __call__(self, *args): + self.response_started = True + self.start_response(*args) + +class CatchingIter(object): + + """ + A wrapper around the application iterator that will catch + exceptions raised by the a generator, or by the close method, and + display or report as necessary. + """ + + def __init__(self, app_iter, environ, start_checker, error_middleware): + self.app_iterable = app_iter + self.app_iterator = iter(app_iter) + self.environ = environ + self.start_checker = start_checker + self.error_middleware = error_middleware + self.closed = False + + def __iter__(self): + return self + + def next(self): + __traceback_supplement__ = ( + Supplement, self.error_middleware, self.environ) + if self.closed: + raise StopIteration + try: + return self.app_iterator.next() + except StopIteration: + self.closed = True + close_response = self._close() + if close_response is not None: + return close_response + else: + raise StopIteration + except: + self.closed = True + close_response = self._close() + exc_info = sys.exc_info() + response = self.error_middleware.exception_handler( + exc_info, self.environ) + if close_response is not None: + response += ( + '<hr noshade>Error in .close():<br>%s' + % close_response) + + if not self.start_checker.response_started: + self.start_checker('500 Internal Server Error', + [('content-type', 'text/html')], + exc_info) + + return response + + def close(self): + # This should at least print something to stderr if the + # close method fails at this point + if not self.closed: + self._close() + + def _close(self): + """Close and return any error message""" + if not hasattr(self.app_iterable, 'close'): + return None + try: + self.app_iterable.close() + return None + except: + close_response = self.error_middleware.exception_handler( + sys.exc_info(), self.environ) + return close_response + + +class Supplement(object): + + """ + This is a supplement used to display standard WSGI information in + the traceback. + """ + + def __init__(self, middleware, environ): + self.middleware = middleware + self.environ = environ + self.source_url = request.construct_url(environ) + + def extraData(self): + data = {} + cgi_vars = data[('extra', 'CGI Variables')] = {} + wsgi_vars = data[('extra', 'WSGI Variables')] = {} + hide_vars = ['paste.config', 'wsgi.errors', 'wsgi.input', + 'wsgi.multithread', 'wsgi.multiprocess', + 'wsgi.run_once', 'wsgi.version', + 'wsgi.url_scheme'] + for name, value in self.environ.items(): + if name.upper() == name: + if value: + cgi_vars[name] = value + elif name not in hide_vars: + wsgi_vars[name] = value + if self.environ['wsgi.version'] != (1, 0): + wsgi_vars['wsgi.version'] = self.environ['wsgi.version'] + proc_desc = tuple([int(bool(self.environ[key])) + for key in ('wsgi.multiprocess', + 'wsgi.multithread', + 'wsgi.run_once')]) + wsgi_vars['wsgi process'] = self.process_combos[proc_desc] + wsgi_vars['application'] = self.middleware.application + if 'paste.config' in self.environ: + data[('extra', 'Configuration')] = dict(self.environ['paste.config']) + return data + + process_combos = { + # multiprocess, multithread, run_once + (0, 0, 0): 'Non-concurrent server', + (0, 1, 0): 'Multithreaded', + (1, 0, 0): 'Multiprocess', + (1, 1, 0): 'Multi process AND threads (?)', + (0, 0, 1): 'Non-concurrent CGI', + (0, 1, 1): 'Multithread CGI (?)', + (1, 0, 1): 'CGI', + (1, 1, 1): 'Multi thread/process CGI (?)', + } + +def handle_exception(exc_info, error_stream, html=True, + debug_mode=False, + error_email=None, + error_log=None, + show_exceptions_in_wsgi_errors=False, + error_email_from='errors@localhost', + smtp_server='localhost', + smtp_username=None, + smtp_password=None, + smtp_use_tls=False, + error_subject_prefix='', + error_message=None, + simple_html_error=False, + environ=None + ): + """ + For exception handling outside of a web context + + Use like:: + + import sys + from paste.exceptions.errormiddleware import handle_exception + try: + do stuff + except: + handle_exception( + sys.exc_info(), sys.stderr, html=False, ...other config...) + + If you want to report, but not fully catch the exception, call + ``raise`` after ``handle_exception``, which (when given no argument) + will reraise the exception. + """ + reported = False + exc_data = collector.collect_exception(*exc_info) + extra_data = '' + if error_email: + rep = reporter.EmailReporter( + to_addresses=error_email, + from_address=error_email_from, + smtp_server=smtp_server, + smtp_username=smtp_username, + smtp_password=smtp_password, + smtp_use_tls=smtp_use_tls, + subject_prefix=error_subject_prefix) + rep_err = send_report(rep, exc_data, html=html) + if rep_err: + extra_data += rep_err + else: + reported = True + if error_log: + rep = reporter.LogReporter( + filename=error_log) + rep_err = send_report(rep, exc_data, html=html) + if rep_err: + extra_data += rep_err + else: + reported = True + if show_exceptions_in_wsgi_errors: + rep = reporter.FileReporter( + file=error_stream) + rep_err = send_report(rep, exc_data, html=html) + if rep_err: + extra_data += rep_err + else: + reported = True + else: + error_stream.write('Error - %s: %s\n' % ( + exc_data.exception_type, exc_data.exception_value)) + if html: + if debug_mode and simple_html_error: + return_error = formatter.format_html( + exc_data, include_hidden_frames=False, + include_reusable=False, show_extra_data=False) + reported = True + elif debug_mode and not simple_html_error: + error_html = formatter.format_html( + exc_data, + include_hidden_frames=True, + include_reusable=False) + head_html = formatter.error_css + formatter.hide_display_js + return_error = error_template( + head_html, error_html, extra_data) + extra_data = '' + reported = True + else: + msg = error_message or ''' + An error occurred. + ''' + extra = "<p><b>The error has been logged to our team.</b>" + if 'sentry_event_id' in environ: + extra += " If you want to contact us about this error, please reference the following<br><br>" + extra += "<b><large>GURU MEDITATION: #" + environ['sentry_event_id'] + "</large></b>" + extra += "</p>" + return_error = error_template('', msg, extra) + else: + return_error = None + if not reported and error_stream: + err_report = formatter.format_text(exc_data, show_hidden_frames=True) + err_report += '\n' + '-'*60 + '\n' + error_stream.write(err_report) + if extra_data: + error_stream.write(extra_data) + return return_error + +def send_report(rep, exc_data, html=True): + try: + rep.report(exc_data) + except: + output = StringIO() + traceback.print_exc(file=output) + if html: + return """ + <p>Additionally an error occurred while sending the %s report: + + <pre>%s</pre> + </p>""" % ( + cgi.escape(str(rep)), output.getvalue()) + else: + return ( + "Additionally an error occurred while sending the " + "%s report:\n%s" % (str(rep), output.getvalue())) + else: + return '' + +def error_template(head_html, exception, extra): + return ''' + <!DOCTYPE HTML> + <html> + <head> + <style type="text/css"> + body { color: #303030; background: #dfe5f9; font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif; font-size:12px; line-height:16px; } + .content { max-width: 720px; margin: auto; margin-top: 50px; } + </style> + <title>Internal Server Error</title> + %s + </head> + <body> + <div class="content"> + <h1>Internal Server Error</h1> + + <h2>Galaxy was unable to sucessfully complete your request</h2> + + <p>%s</p> + + This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. + + %s + </div> + </body> + </html>''' % (head_html, exception, extra) + +def make_error_middleware(app, global_conf, **kw): + return ErrorMiddleware(app, global_conf=global_conf, **kw) + +doc_lines = ErrorMiddleware.__doc__.splitlines(True) +for i in range(len(doc_lines)): + if doc_lines[i].strip().startswith('Settings'): + make_error_middleware.__doc__ = ''.join(doc_lines[i:]) + break +del i, doc_lines \ No newline at end of file diff -r fc99a36f9d2195bc742f6e557ae56b7b61ad6766 -r d2b192832826f531e7702461826822dbb8179acb lib/galaxy/web/framework/middleware/sentry.py --- /dev/null +++ b/lib/galaxy/web/framework/middleware/sentry.py @@ -0,0 +1,70 @@ +""" +raven.middleware +~~~~~~~~~~~~~~~~~~~~~~~~ + +:copyright: (c) 2010-2012 by the Sentry Team, see AUTHORS for more details. +:license: BSD, see LICENSE for more details. +""" + +import galaxy.eggs; galaxy.eggs.require( "raven" ) + +from raven import Client +from raven.utils.wsgi import get_current_url, get_headers, \ + get_environ + +class Sentry(object): + """ + A WSGI middleware which will attempt to capture any + uncaught exceptions and send them to Sentry. + + >>> from raven.base import Client + >>> application = Sentry(application, Client()) + """ + def __init__(self, application, dsn): + self.application = application + self.client = Client( dsn ) + + def __call__(self, environ, start_response): + try: + iterable = self.application(environ, start_response) + except Exception: + self.handle_exception(environ) + raise + + try: + for event in iterable: + yield event + except Exception: + self.handle_exception(environ) + raise + finally: + # wsgi spec requires iterable to call close if it exists + # see http://blog.dscpl.com.au/2012/10/obligations-for-calling-close-on.html + if iterable and hasattr(iterable, 'close') and callable(iterable.close): + try: + iterable.close() + except Exception: + self.handle_exception(environ) + + def handle_exception(self, environ): + event_id = self.client.captureException( + data={ + 'sentry.interfaces.Http': { + 'method': environ.get('REQUEST_METHOD'), + 'url': get_current_url(environ, strip_querystring=True), + 'query_string': environ.get('QUERY_STRING'), + # TODO + # 'data': environ.get('wsgi.input'), + 'headers': dict(get_headers(environ)), + 'env': dict(get_environ(environ)), + } + }, + # Galaxy: add request id from environment if available + extra={ + 'request_id': environ.get( 'request_id', 'Unknown' ) + } + ) + # Galaxy: store event_id in environment so we can show it to the user + environ['sentry_event_id'] = event_id[0] + + return event_id \ No newline at end of file diff -r fc99a36f9d2195bc742f6e557ae56b7b61ad6766 -r d2b192832826f531e7702461826822dbb8179acb lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -242,12 +242,10 @@ log.debug( "Enabling 'recursive' middleware" ) # If sentry logging is enabled, log here before propogating up to # the error middleware - sentry_url = conf.get( 'sentry_url', None ) - if sentry_url: - pkg_resources.require( "raven") - from raven import Client - from raven.middleware import Sentry - app = Sentry( app, Client( sentry_url ) ) + sentry_dsn = conf.get( 'sentry_dsn', None ) + if sentry_dsn: + from galaxy.web.framework.middleware.sentry import Sentry + app = Sentry( app, sentry_dsn ) # Various debug middleware that can only be turned on if the debug # flag is set, either because they are insecure or greatly hurt # performance @@ -275,11 +273,11 @@ # Not in interactive debug mode, just use the regular error middleware if sys.version_info[:2] >= ( 2, 6 ): warnings.filterwarnings( 'ignore', '.*', DeprecationWarning, '.*serial_number_generator', 11, True ) - from paste.exceptions import errormiddleware + import galaxy.web.framework.middleware.error warnings.filters.pop() else: - from paste.exceptions import errormiddleware - app = errormiddleware.ErrorMiddleware( app, conf ) + import galaxy.web.framework.middleware.error + app = galaxy.web.framework.middleware.error.ErrorMiddleware( app, conf ) log.debug( "Enabling 'error' middleware" ) # Transaction logging (apache access.log style) if asbool( conf.get( 'use_translogger', True ) ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: james_taylor: Fix leftover debug code
by Bitbucket 02 Feb '13

02 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fc99a36f9d21/ changeset: fc99a36f9d21 user: james_taylor date: 2013-02-03 00:29:05 summary: Fix leftover debug code affected #: 2 files diff -r 708d0ccee63fc75eb88e5dc3a9e0d6d3e5ff72e7 -r fc99a36f9d2195bc742f6e557ae56b7b61ad6766 templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -54,7 +54,7 @@ ${h.js( "mvc/ui" )} - + <script type="text/javascript"> // console protection window.console = window.console || { diff -r 708d0ccee63fc75eb88e5dc3a9e0d6d3e5ff72e7 -r fc99a36f9d2195bc742f6e557ae56b7b61ad6766 templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -74,7 +74,7 @@ }); */ - $( '.tooltip' ).tooltip().foasdasdasdoo(); + $( '.tooltip' ).tooltip(); // TODO: is this necessary? $( "a[minsizehint]" ).click( function() { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: james_taylor: Support for using Sentry for error logging. If sentry_dsn is set in
by Bitbucket 02 Feb '13

02 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/708d0ccee63f/ changeset: 708d0ccee63f user: james_taylor date: 2013-02-02 23:56:55 summary: Support for using Sentry for error logging. If sentry_dsn is s= et in universe_wsgi.ini, then: - A middleware will be installed that send thrown exceptions to sentry - All logging messages of level WARN and above will be sent to sentry - All pages extending base/base_panels will have javascript errors captured and sent to sentry affected #: 11 files diff -r 7950ce95b2769f2fb63bfc8a549ee9bc9fdcbed2 -r 708d0ccee63fc75eb88e5dc= 3a9e0d6d3e5ff72e7 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -66,6 +66,7 @@ wchartype =3D 0.1 Whoosh =3D 0.3.18 ; fluent_logger =3D 0.3.3 +raven =3D 3.1.8 =20 ; extra version information [tags] diff -r 7950ce95b2769f2fb63bfc8a549ee9bc9fdcbed2 -r 708d0ccee63fc75eb88e5dc= 3a9e0d6d3e5ff72e7 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -2,7 +2,7 @@ Universe configuration builder. """ =20 -import sys, os, tempfile +import sys, os, tempfile, re import logging, logging.config import ConfigParser from datetime import timedelta @@ -261,11 +261,24 @@ self.api_folders =3D string_as_bool( kwargs.get( 'api_folders', Fa= lse ) ) # This is for testing new library browsing capabilities. self.new_lib_browse =3D string_as_bool( kwargs.get( 'new_lib_brows= e', False ) ) + # Error logging with sentry + self.sentry_dsn =3D kwargs.get( 'sentry_dsn', None ) # Logging with fluentd self.fluent_log =3D string_as_bool( kwargs.get( 'fluent_log', Fals= e ) ) self.fluent_host =3D kwargs.get( 'fluent_host', 'localhost' ) self.fluent_port =3D int( kwargs.get( 'fluent_port', 24224 ) ) =20 + @property + def sentry_dsn_public( self ): + """ + Sentry URL with private key removed for use in client side scripts= ,=20 + sentry server will need to be configured to accept events + """ + if self.sentry_dsn: + return re.sub( r"^([^:/?#]+:)?//(\w+):(\w+)", r"\1//\2", self.= sentry_dsn ) + else: + return None + def __read_tool_job_config( self, global_conf_parser, section, key ): try: tool_runners_config =3D global_conf_parser.items( section ) @@ -387,8 +400,7 @@ =20 def configure_logging( config ): """ - Allow some basic logging configuration to be read from the cherrpy - config. + Allow some basic logging configuration to be read from ini file. """ # PasteScript will have already configured the logger if the appropria= te # sections were found in the config file, so we do nothing if the @@ -420,3 +432,10 @@ # Hook everything up handler.setFormatter( formatter ) root.addHandler( handler ) + # If sentry is configured, also log to it + if config.sentry_dsn: + pkg_resources.require( "raven" ) + from raven.handlers.logging import SentryHandler + sentry_handler =3D SentryHandler( config.sentry_dsn ) + sentry_handler.setLevel( logging.WARN ) + root.addHandler( sentry_handler ) diff -r 7950ce95b2769f2fb63bfc8a549ee9bc9fdcbed2 -r 708d0ccee63fc75eb88e5dc= 3a9e0d6d3e5ff72e7 lib/galaxy/web/framework/base.py --- a/lib/galaxy/web/framework/base.py +++ b/lib/galaxy/web/framework/base.py @@ -9,7 +9,6 @@ import sys import tarfile import threading -import uuid =20 from Cookie import SimpleCookie =20 @@ -70,9 +69,6 @@ self.mapper.explicit =3D False self.api_mapper =3D routes.Mapper() self.transaction_factory =3D DefaultWebTransaction - # Each request will have a unique id. Since we are assuming - # a threaded model for the moment we can store that here - self.request_id =3D threading.local() # Set if trace logging is enabled self.trace_logger =3D None def add_ui_controller( self, controller_name, controller ): @@ -124,7 +120,7 @@ and calls it. """ # Immediately create request_id which we will use for logging - self.request_id =3D request_id =3D uuid.uuid1().hex + request_id =3D environ.get( 'request_id', 'unknown' ) if self.trace_logger: self.trace_logger.context_set( "request_id", request_id ) self.trace( message=3D"Starting request" ) @@ -136,6 +132,8 @@ self.trace_logger.context_remove( "request_id" ) =20 def handle_request( self, environ, start_response ): + # Grab the request_id (should have been set by middleware) + request_id =3D environ.get( 'request_id', 'unknown' ) # Map url using routes path_info =3D environ.get( 'PATH_INFO', '' ) map =3D self.mapper.match( path_info, environ ) @@ -157,6 +155,7 @@ rc.environ =3D environ # Setup the transaction trans =3D self.transaction_factory( environ ) + trans.request_id =3D request_id rc.redirect =3D trans.response.send_redirect # Get the controller class controller_name =3D map.pop( 'controller', None ) diff -r 7950ce95b2769f2fb63bfc8a549ee9bc9fdcbed2 -r 708d0ccee63fc75eb88e5dc= 3a9e0d6d3e5ff72e7 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -240,6 +240,14 @@ from paste import recursive app =3D recursive.RecursiveMiddleware( app, conf ) log.debug( "Enabling 'recursive' middleware" ) + # If sentry logging is enabled, log here before propogating up to + # the error middleware + sentry_url =3D conf.get( 'sentry_url', None ) + if sentry_url: + pkg_resources.require( "raven") + from raven import Client + from raven.middleware import Sentry + app =3D Sentry( app, Client( sentry_url ) ) # Various debug middleware that can only be turned on if the debug # flag is set, either because they are insecure or greatly hurt # performance @@ -254,12 +262,6 @@ from paste.debug import profile app =3D profile.ProfileMiddleware( app, conf ) log.debug( "Enabling 'profile' middleware" ) - # Middleware that intercepts print statements and shows them on the - # returned page - if asbool( conf.get( 'use_printdebug', True ) ): - from paste.debug import prints - app =3D prints.PrintDebugMiddleware( app, conf ) - log.debug( "Enabling 'print debug' middleware" ) if debug and asbool( conf.get( 'use_interactive', False ) ): # Interactive exception debugging, scary dangerous if publicly # accessible, if not enabled we'll use the regular error printing @@ -288,6 +290,10 @@ from galaxy.web.framework.middleware.xforwardedhost import XForwardedH= ostMiddleware app =3D XForwardedHostMiddleware( app ) log.debug( "Enabling 'x-forwarded-host' middleware" ) + # Request ID middleware + from galaxy.web.framework.middleware.request_id import RequestIDMiddle= ware + app =3D RequestIDMiddleware( app ) + log.debug( "Enabling 'Request ID' middleware" ) return app =20 def wrap_in_static( app, global_conf, **local_conf ): diff -r 7950ce95b2769f2fb63bfc8a549ee9bc9fdcbed2 -r 708d0ccee63fc75eb88e5dc= 3a9e0d6d3e5ff72e7 static/scripts/libs/raven.js --- /dev/null +++ b/static/scripts/libs/raven.js @@ -0,0 +1,438 @@ +(function(){ + +// Raven.js +// +// Originally based on the Arecibo JavaScript client. +// +// Requires: +// * TraceKit (included in the full and minified distribution files) + +'use strict'; + +// First, check for JSON support +// If there is no JSON, we no-op the core features of Raven +// since JSON is required to encode the payload +var _Raven =3D window.Raven, + hasJSON =3D !isUndefined(window.JSON), + globalServer, + globalUser, + globalKey, + globalProject, + globalOptions =3D { + logger: 'javascript', + ignoreErrors: [], + ignoreUrls: [] + }; + +var TK =3D TraceKit.noConflict(); + +// Disable Tracekit's remote fetching by default +TK.remoteFetching =3D false; + +/* + * The core Raven object + */ +var Raven =3D { + VERSION: '@VERSION', + + /* + * Raven.noConflict() + * + * Allow multiple versions of Raven to be installed. + */ + noConflict: function() { + window.Raven =3D _Raven; + return Raven; + }, + + /* + * Raven.config() + * + * Configure raven with a DSN and extra options + */ + config: function(dsn, options) { + var uri =3D parseUri(dsn), + lastSlash =3D uri.path.lastIndexOf('/'), + path =3D uri.path.substr(1, lastSlash); + + // merge in options + if (options) { + each(options, function(key, value){ + globalOptions[key] =3D value; + }); + } + + // "Script error." is hard coded into browsers for errors that it = can't read. + // this is the result of a script being pulled in from an external= domain and CORS. + globalOptions.ignoreErrors.push('Script error.'); + + globalKey =3D uri.user; + globalProject =3D ~~uri.path.substr(lastSlash + 1); + + // assemble the endpoint from the uri pieces + globalServer =3D uri.protocol + '://' + uri.host + + (uri.port ? ':' + uri.port : '') + + '/' + path + 'api/' + globalProject + '/store/'; + + if (globalOptions.fetchContext) { + TK.remoteFetching =3D true; + } + + // return for chaining + return Raven; + }, + + /* + * Raven.install() + * + * Installs a global window.onerror error handler + * to capture and report uncaught exceptions. + */ + install: function() { + if (!isSetup()) return; + + TK.report.subscribe(handleStackInfo); + + return Raven; + }, + + /* + * Raven.context() + * + * Wrap code within a context so Raven can capture errors + * reliably across domains that is executed immediately. + */ + context: function(options, func, args) { + if (isFunction(options)) { + args =3D func; + func =3D options; + options =3D undefined; + } + + Raven.wrap(options, func).apply(this, args); + }, + + /* Raven.wrap() + * + * Wrap code within a context and returns back a new function to be ex= ecuted + */ + wrap: function(options, func) { + // options is optional + if (isFunction(options)) { + func =3D options; + options =3D undefined; + } + + return function() { + try { + func.apply(this, arguments); + } catch(e) { + Raven.captureException(e, options); + } + }; + }, + + /* + * Raven.uninstall() + * + * Uninstalls the global error handler. + */ + uninstall: function() { + TK.report.unsubscribe(handleStackInfo); + + return Raven; + }, + + /* + * Raven.captureException() + * + * Manually capture an exception and send it over to Sentry + */ + captureException: function(ex, options) { + // TraceKit.report will re-raise any exception passed to it, + // which means you have to wrap it in try/catch. Instead, we + // can wrap it here and only re-raise if TraceKit.report + // raises an exception different from the one we asked to + // report on. + try { + TK.report(ex, options); + } catch(ex1) { + if(ex !=3D=3D ex1) { + throw ex1; + } + } + + return Raven; + }, + + /* + * Raven.captureMessage() + * + * Manually send a message to Sentry + */ + captureMessage: function(msg, options) { + // Fire away! + send( + arrayMerge({ + message: msg + }, options) + ); + + return Raven; + }, + + /* + * Raven.setUser() + * + * Set/clear a user to be sent along with the payload. + */ + setUser: function(user) { + globalUser =3D user; + + return Raven; + } +}; + +var uriKeys =3D 'source protocol authority userInfo user password host por= t relative path directory file query anchor'.split(' '), + uriPattern =3D /^(?:(?![^:@]+:[^:@\/]*@)([^:\/?#.]+):)?(?:\/\/)?((?:((= [^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?)(((\/(?:[^?#](?![^?#\/]*\.= [^?#\/.]+(?:[?#]|$)))*\/?)?([^?#\/]*))(?:\?([^#]*))?(?:#(.*))?)/; + +/**** Private functions ****/ +function parseUri(str) { + var m =3D uriPattern.exec(str), + uri =3D {}, + i =3D 14; + + while (i--) uri[uriKeys[i]] =3D m[i] || ''; + + return uri; +} + +function isUndefined(what) { + return typeof what =3D=3D=3D 'undefined'; +} + +function isFunction(what) { + return typeof what =3D=3D=3D 'function'; +} + +function each(obj, callback) { + var i, j; + + if (obj.length =3D=3D=3D undefined) { + for (i in obj) { + if (obj.hasOwnProperty(i)) { + callback.call(null, i, obj[i]); + } + } + } else { + for (i =3D 0, j =3D obj.length; i < j; i++) { + callback.call(null, i, obj[i]); + } + } +} + +var cachedAuth; + +function getAuthQueryString() { + if (cachedAuth) return cachedAuth; + + var qs =3D [ + 'sentry_version=3D2.0', + 'sentry_client=3Draven-js/' + Raven.VERSION + ]; + if (globalKey) { + qs.push('sentry_key=3D' + globalKey); + } + + cachedAuth =3D '?' + qs.join('&'); + return cachedAuth; +} + +function handleStackInfo(stackInfo, options) { + var frames =3D [], i =3D 0, j =3D stackInfo.stack && stackInfo.stack.l= ength || 0, frame; + + for (; i < j; i++) { + frame =3D normalizeFrame(stackInfo.stack[i]); + if (frame) { + frames.push(frame); + } + } + + processException( + stackInfo.name, + stackInfo.message, + stackInfo.url, + stackInfo.lineno, + frames, + options + ); +} + +function normalizeFrame(frame) { + if (!frame.url) return; + + // normalize the frames data + var normalized =3D { + filename: frame.url, + lineno: frame.line, + colno: frame.column, + 'function': frame.func || '?' + }, context =3D extractContextFromFrame(frame); + + if (context) { + var i =3D 3, keys =3D ['pre_context', 'context_line', 'post_contex= t']; + while (i--) normalized[keys[i]] =3D context[i]; + } + + normalized.in_app =3D !/(Raven|TraceKit)\./.test(normalized['function'= ]); + + return normalized; +} + +function extractContextFromFrame(frame) { + // immediately check if we should even attempt to parse a context + if (!frame.context || !globalOptions.fetchContext) return; + + var context =3D frame.context, + pivot =3D ~~(context.length / 2), + i =3D context.length, isMinified =3D false; + + while (i--) { + // We're making a guess to see if the source is minified or not. + // To do that, we make the assumption if *any* of the lines passed + // in are greater than 300 characters long, we bail. + // Sentry will see that there isn't a context + if (context[i].length > 300) { + isMinified =3D true; + break; + } + } + + if (isMinified) { + // The source is minified and we don't know which column. Fuck it. + if (isUndefined(frame.column)) return; + + // If the source is minified and has a frame column + // we take a chunk of the offending line to hopefully shed some li= ght + return [ + [], // no pre_context + context[pivot].substr(frame.column, 50), // grab 50 characters= , starting at the offending column + [] // no post_context + ]; + } + + return [ + context.slice(0, pivot), // pre_context + context[pivot], // context_line + context.slice(pivot + 1) // post_context + ]; +} + +function processException(type, message, fileurl, lineno, frames, options)= { + var stacktrace, label, i; + + // IE8 really doesn't have Array.prototype.indexOf + // Filter out a message that matches our ignore list + i =3D globalOptions.ignoreErrors.length; + while (i--) { + if (message =3D=3D=3D globalOptions.ignoreErrors[i]) { + return; + } + } + + if (frames && frames.length) { + stacktrace =3D {frames: frames}; + fileurl =3D fileurl || frames[0].filename; + } else if (fileurl) { + stacktrace =3D { + frames: [{ + filename: fileurl, + lineno: lineno + }] + }; + } + + i =3D globalOptions.ignoreUrls.length; + while (i--) { + if (globalOptions.ignoreUrls[i].test(fileurl)) { + return; + } + } + + label =3D lineno ? message + ' at ' + lineno : message; + + // Fire away! + send( + arrayMerge({ + 'sentry.interfaces.Exception': { + type: type, + value: message + }, + 'sentry.interfaces.Stacktrace': stacktrace, + culprit: fileurl, + message: label + }, options) + ); +} + +function arrayMerge(arr1, arr2) { + if (!arr2) { + return arr1; + } + each(arr2, function(key, value){ + arr1[key] =3D value; + }); + return arr1; +} + +function getHttpData() { + var http =3D { + url: window.location.href, + headers: { + 'User-Agent': navigator.userAgent + } + }; + + if (window.document.referrer) { + http.headers.Referer =3D window.document.referrer; + } + + return http; +} + +function send(data) { + if (!isSetup()) return; + + data =3D arrayMerge({ + project: globalProject, + logger: globalOptions.logger, + site: globalOptions.site, + platform: 'javascript', + 'sentry.interfaces.Http': getHttpData() + }, data ); + + if (globalUser) data['sentry.interfaces.User'] =3D globalUser; + + if (isFunction(globalOptions.dataCallback)) { + data =3D globalOptions.dataCallback(data); + } + + makeRequest(data); +} + +function makeRequest(data) { + new Image().src =3D globalServer + getAuthQueryString() + '&sentry_dat= a=3D' + encodeURIComponent(JSON.stringify(data)); +} + +function isSetup() { + if (!hasJSON) return false; // needs JSON support + if (!globalServer) { + console.error("Error: Raven has not been configured."); + return false; + } + return true; +} + +window.Raven =3D Raven; + +})(); diff -r 7950ce95b2769f2fb63bfc8a549ee9bc9fdcbed2 -r 708d0ccee63fc75eb88e5dc= 3a9e0d6d3e5ff72e7 static/scripts/libs/tracekit.js --- /dev/null +++ b/static/scripts/libs/tracekit.js @@ -0,0 +1,1210 @@ +/* + TraceKit - Cross brower stack traces - github.com/occ/TraceKit + MIT license +*/ + +;(function(window, undefined) { + + +var TraceKit =3D {}; +var _oldTraceKit =3D window.TraceKit; + +/** + * TraceKit.noConflict: Export TraceKit out to another variable + * Example: var TK =3D TraceKit.noConflict() + */ +TraceKit.noConflict =3D function noConflict() { + window.TraceKit =3D _oldTraceKit; + return TraceKit; +}; + +/** + * TraceKit._has, a better form of hasOwnProperty + * Example: TraceKit._has(MainHostObject, property) =3D=3D=3D true/false + * + * @param {Object} host object to check property + * @param {string} key to check + */ +TraceKit._has =3D function _has(object, key) { + return Object.prototype.hasOwnProperty.call(object, key); +}; + +/** + * TraceKit.report: cross-browser processing of unhandled exceptions + * + * Syntax: + * TraceKit.report.subscribe(function(stackInfo) { ... }) + * TraceKit.report.unsubscribe(function(stackInfo) { ... }) + * TraceKit.report(exception) + * try { ...code... } catch(ex) { TraceKit.report(ex); } + * + * Supports: + * - Firefox: full stack trace with line numbers, plus column number + * on top frame; column number is not guaranteed + * - Opera: full stack trace with line and column numbers + * - Chrome: full stack trace with line and column numbers + * - Safari: line and column number for the top frame only; some frames + * may be missing, and column number is not guaranteed + * - IE: line and column number for the top frame only; some frames + * may be missing, and column number is not guaranteed + * + * In theory, TraceKit should work on all of the following versions: + * - IE5.5+ (only 8.0 tested) + * - Firefox 0.9+ (only 3.5+ tested) + * - Opera 7+ (only 10.50 tested; versions 9 and earlier may require + * Exceptions Have Stacktrace to be enabled in opera:config) + * - Safari 3+ (only 4+ tested) + * - Chrome 1+ (only 5+ tested) + * - Konqueror 3.5+ (untested) + * + * Requires TraceKit.computeStackTrace. + * + * Tries to catch all unhandled exceptions and report them to the + * subscribed handlers. Please note that TraceKit.report will rethrow the + * exception. This is REQUIRED in order to get a useful stack trace in IE. + * If the exception does not reach the top of the browser, you will only + * get a stack trace from the point where TraceKit.report was called. + * + * Handlers receive a stackInfo object as described in the + * TraceKit.computeStackTrace docs. + */ +TraceKit.report =3D (function reportModuleWrapper() { + var handlers =3D [], + lastException =3D null, + lastExceptionStack =3D null; + + /** + * Add a crash handler. + * @param {Function} handler + */ + function subscribe(handler) { + handlers.push(handler); + } + + /** + * Remove a crash handler. + * @param {Function} handler + */ + function unsubscribe(handler) { + for (var i =3D handlers.length - 1; i >=3D 0; --i) { + if (handlers[i] =3D=3D=3D handler) { + handlers.splice(i, 1); + } + } + } + + /** + * Dispatch stack information to all handlers. + * @param {Object.<string, *>} stack + */ + function notifyHandlers(stack, windowError) { + var exception =3D null; + if (windowError && !TraceKit.collectWindowErrors) { + return; + } + for (var i in handlers) { + if (TraceKit._has(handlers, i)) { + try { + handlers[i].apply(null, [stack].concat(Array.prototype= .slice.call(arguments, 2))); + } catch (inner) { + exception =3D inner; + } + } + } + + if (exception) { + throw exception; + } + } + + var _oldOnerrorHandler =3D window.onerror; + + /** + * Ensures all global unhandled exceptions are recorded. + * Supported by Gecko and IE. + * @param {string} message Error message. + * @param {string} url URL of script that generated the exception. + * @param {(number|string)} lineNo The line number at which the error + * occurred. + */ + window.onerror =3D function traceKitWindowOnError(message, url, lineNo= ) { + var stack =3D null; + + if (lastExceptionStack) { + TraceKit.computeStackTrace.augmentStackTraceWithInitialElement= (lastExceptionStack, url, lineNo, message); + stack =3D lastExceptionStack; + lastExceptionStack =3D null; + lastException =3D null; + } else { + var location =3D { + 'url': url, + 'line': lineNo + }; + location.func =3D TraceKit.computeStackTrace.guessFunctionName= (location.url, location.line); + location.context =3D TraceKit.computeStackTrace.gatherContext(= location.url, location.line); + stack =3D { + 'mode': 'onerror', + 'message': message, + 'url': document.location.href, + 'stack': [location], + 'useragent': navigator.userAgent + }; + } + + notifyHandlers(stack, 'from window.onerror'); + + if (_oldOnerrorHandler) { + return _oldOnerrorHandler.apply(this, arguments); + } + + return false; + }; + + /** + * Reports an unhandled Error to TraceKit. + * @param {Error} ex + */ + function report(ex) { + var args =3D Array.prototype.slice.call(arguments, 1); + if (lastExceptionStack) { + if (lastException =3D=3D=3D ex) { + return; // already caught by an inner catch block, ignore + } else { + var s =3D lastExceptionStack; + lastExceptionStack =3D null; + lastException =3D null; + notifyHandlers.apply(null, [s, null].concat(args)); + } + } + + var stack =3D TraceKit.computeStackTrace(ex); + lastExceptionStack =3D stack; + lastException =3D ex; + + // If the stack trace is incomplete, wait for 2 seconds for + // slow slow IE to see if onerror occurs or not before reporting + // this exception; otherwise, we will end up with an incomplete + // stack trace + window.setTimeout(function () { + if (lastException =3D=3D=3D ex) { + lastExceptionStack =3D null; + lastException =3D null; + notifyHandlers.apply(null, [stack, null].concat(args)); + } + }, (stack.incomplete ? 2000 : 0)); + + throw ex; // re-throw to propagate to the top level (and cause win= dow.onerror) + } + + report.subscribe =3D subscribe; + report.unsubscribe =3D unsubscribe; + return report; +}()); + +/** + * TraceKit.computeStackTrace: cross-browser stack traces in JavaScript + * + * Syntax: + * s =3D TraceKit.computeStackTrace.ofCaller([depth]) + * s =3D TraceKit.computeStackTrace(exception) // consider using TraceKi= t.report instead (see below) + * Returns: + * s.name - exception name + * s.message - exception message + * s.stack[i].url - JavaScript or HTML file URL + * s.stack[i].func - function name, or empty for anonymous functions= (if guessing did not work) + * s.stack[i].args - arguments passed to the function, if known + * s.stack[i].line - line number, if known + * s.stack[i].column - column number, if known + * s.stack[i].context - an array of source code lines; the middle eleme= nt corresponds to the correct line# + * s.mode - 'stack', 'stacktrace', 'multiline', 'callers', = 'onerror', or 'failed' -- method used to collect the stack trace + * + * Supports: + * - Firefox: full stack trace with line numbers and unreliable column + * number on top frame + * - Opera 10: full stack trace with line and column numbers + * - Opera 9-: full stack trace with line numbers + * - Chrome: full stack trace with line and column numbers + * - Safari: line and column number for the topmost stacktrace element + * only + * - IE: no line numbers whatsoever + * + * Tries to guess names of anonymous functions by looking for assignments + * in the source code. In IE and Safari, we have to guess source file names + * by searching for function bodies inside all page scripts. This will not + * work for scripts that are loaded cross-domain. + * Here be dragons: some function names may be guessed incorrectly, and + * duplicate functions may be mismatched. + * + * TraceKit.computeStackTrace should only be used for tracing purposes. + * Logging of unhandled exceptions should be done with TraceKit.report, + * which builds on top of TraceKit.computeStackTrace and provides better + * IE support by utilizing the window.onerror event to retrieve information + * about the top of the stack. + * + * Note: In IE and Safari, no stack trace is recorded on the Error object, + * so computeStackTrace instead walks its *own* chain of callers. + * This means that: + * * in Safari, some methods may be missing from the stack trace; + * * in IE, the topmost function in the stack trace will always be the + * caller of computeStackTrace. + * + * This is okay for tracing (because you are likely to be calling + * computeStackTrace from the function you want to be the topmost element + * of the stack trace anyway), but not okay for logging unhandled + * exceptions (because your catch block will likely be far away from the + * inner function that actually caused the exception). + * + * Tracing example: + * function trace(message) { + * var stackInfo =3D TraceKit.computeStackTrace.ofCaller(); + * var data =3D message + "\n"; + * for(var i in stackInfo.stack) { + * var item =3D stackInfo.stack[i]; + * data +=3D (item.func || '[anonymous]') + "() in " + item.ur= l + ":" + (item.line || '0') + "\n"; + * } + * if (window.console) + * console.info(data); + * else + * alert(data); + * } + */ +TraceKit.computeStackTrace =3D (function computeStackTraceWrapper() { + var debug =3D false, + sourceCache =3D {}; + + /** + * Attempts to retrieve source code via XMLHttpRequest, which is used + * to look up anonymous function names. + * @param {string} url URL of source code. + * @return {string} Source contents. + */ + function loadSource(url) { + if (!TraceKit.remoteFetching) { //Only attempt request if remoteFe= tching is on. + return ''; + } + try { + var XMLHttpRequestWrapper; + + if (typeof (XMLHttpRequest) =3D=3D=3D 'undefined') { // IE 5.x= -6.x: + XMLHttpRequestWrapper =3D function IEXMLHttpRequestSub() { + try { + return new ActiveXObject('Msxml2.XMLHTTP.6.0'); + } catch (e) {} + try { + return new ActiveXObject('Msxml2.XMLHTTP.3.0'); + } catch (e) {} + try { + return new ActiveXObject('Msxml2.XMLHTTP'); + } catch (e) {} + try { + return new ActiveXObject('Microsoft.XMLHTTP'); + } catch (e) {} + throw new Error('No XHR.'); + }; + } else { + XMLHttpRequestWrapper =3D XMLHttpRequest; + } + =20 + var request =3D new XMLHttpRequestWrapper(); + request.open('GET', url, false); + request.send(''); + return request.responseText; + } catch (e) { + return ''; + } + } + + /** + * Retrieves source code from the source code cache. + * @param {string} url URL of source code. + * @return {Array.<string>} Source contents. + */ + function getSource(url) { + if (!TraceKit._has(sourceCache, url)) { + // URL needs to be able to fetched within the acceptable domai= n. Otherwise, + // cross-domain errors will be triggered. + var source; + if (url.indexOf(document.domain) !=3D=3D -1) { + source =3D loadSource(url); + } else { + source =3D []; + } + sourceCache[url] =3D source.length ? source.split('\n') : []; + } + + return sourceCache[url]; + } + + /** + * Tries to use an externally loaded copy of source code to determine + * the name of a function by looking at the name of the variable it was + * assigned to, if any. + * @param {string} url URL of source code. + * @param {(string|number)} lineNo Line number in source code. + * @return {string} The function name, if discoverable. + */ + function guessFunctionName(url, lineNo) { + var reFunctionArgNames =3D /function ([^(]*)$([^)]*)$/, + reGuessFunction =3D /['"]?([0-9A-Za-z$_]+)['"]?\s*[:=3D]\s*(fu= nction|eval|new Function)/, + line =3D '', + maxLines =3D 10, + source =3D getSource(url), + m; + + if (!source.length) { + return '?'; + } + + // Walk backwards from the first line in the function until we fin= d the line which + // matches the pattern above, which is the function definition + for (var i =3D 0; i < maxLines; ++i) { + line =3D source[lineNo - i] + line; + + if (line !=3D=3D undefined) { + if ((m =3D reGuessFunction.exec(line))) { + return m[1]; + } else if ((m =3D reFunctionArgNames.exec(line))) { + return m[1]; + } + } + } + + return '?'; + } + + /** + * Retrieves the surrounding lines from where an exception occurred. + * @param {string} url URL of source code. + * @param {(string|number)} line Line number in source code to centre + * around for context. + * @return {?Array.<string>} Lines of source code. + */ + function gatherContext(url, line) { + var source =3D getSource(url); + + if (!source.length) { + return null; + } + + var context =3D [], + // linesBefore & linesAfter are inclusive with the offending l= ine. + // if linesOfContext is even, there will be one extra line + // *before* the offending line. + linesBefore =3D Math.floor(TraceKit.linesOfContext / 2), + // Add one extra line if linesOfContext is odd + linesAfter =3D linesBefore + (TraceKit.linesOfContext % 2), + start =3D Math.max(0, line - linesBefore - 1), + end =3D Math.min(source.length, line + linesAfter - 1); + + line -=3D 1; // convert to 0-based index + + for (var i =3D start; i < end; ++i) { + if (typeof (source[i]) !=3D=3D 'undefined') { + context.push(source[i]); + } + } + + return context.length > 0 ? context : null; + } + + /** + * Escapes special characters, except for whitespace, in a string to be + * used inside a regular expression as a string literal. + * @param {string} text The string. + * @return {string} The escaped string literal. + */ + function escapeRegExp(text) { + return text.replace(/[\-\[\]{}()*+?.,\\\^$|#]/g, '\\$&'); + } + + /** + * Escapes special characters in a string to be used inside a regular + * expression as a string literal. Also ensures that HTML entities will + * be matched the same as their literal friends. + * @param {string} body The string. + * @return {string} The escaped string. + */ + function escapeCodeAsRegExpForMatchingInsideHTML(body) { + return escapeRegExp(body).replace('<', '(?:<|<)').replace('>', = '(?:>|>)').replace('&', '(?:&|&)').replace('"', '(?:"|")').repl= ace(/\s+/g, '\\s+'); + } + + /** + * Determines where a code fragment occurs in the source code. + * @param {RegExp} re The function definition. + * @param {Array.<string>} urls A list of URLs to search. + * @return {?Object.<string, (string|number)>} An object containing + * the url, line, and column number of the defined function. + */ + function findSourceInUrls(re, urls) { + var source, m; + for (var i =3D 0, j =3D urls.length; i < j; ++i) { + // console.log('searching', urls[i]); + if ((source =3D getSource(urls[i])).length) { + source =3D source.join('\n'); + if ((m =3D re.exec(source))) { + // console.log('Found function in ' + urls[i]); + + return { + 'url': urls[i], + 'line': source.substring(0, m.index).split('\n').l= ength, + 'column': m.index - source.lastIndexOf('\n', m.ind= ex) - 1 + }; + } + } + } + + // console.log('no match'); + + return null; + } + + /** + * Determines at which column a code fragment occurs on a line of the + * source code. + * @param {string} fragment The code fragment. + * @param {string} url The URL to search. + * @param {(string|number)} line The line number to examine. + * @return {?number} The column number. + */ + function findSourceInLine(fragment, url, line) { + var source =3D getSource(url), + re =3D new RegExp('\\b' + escapeRegExp(fragment) + '\\b'), + m; + + line -=3D 1; + + if (source && source.length > line && (m =3D re.exec(source[line])= )) { + return m.index; + } + + return null; + } + + /** + * Determines where a function was defined within the source code. + * @param {(Function|string)} func A function reference or serialized + * function definition. + * @return {?Object.<string, (string|number)>} An object containing + * the url, line, and column number of the defined function. + */ + function findSourceByFunctionBody(func) { + var urls =3D [window.location.href], + scripts =3D document.getElementsByTagName('script'), + body, + code =3D '' + func, + codeRE =3D /^function(?:\s+([\w$]+))?\s*$([\w\s,]*)$\s*\{\s*= (\S[\s\S]*\S)\s*\}\s*$/, + eventRE =3D /^function on([\w$]+)\s*$event$\s*\{\s*(\S[\s\S]= *\S)\s*\}\s*$/, + re, + parts, + result; + + for (var i =3D 0; i < scripts.length; ++i) { + var script =3D scripts[i]; + if (script.src) { + urls.push(script.src); + } + } + + if (!(parts =3D codeRE.exec(code))) { + re =3D new RegExp(escapeRegExp(code).replace(/\s+/g, '\\s+')); + } + + // not sure if this is really necessary, but I don=E2=80=99t have = a test + // corpus large enough to confirm that and it was in the original. + else { + var name =3D parts[1] ? '\\s+' + parts[1] : '', + args =3D parts[2].split(',').join('\\s*,\\s*'); + + body =3D escapeRegExp(parts[3]).replace(/;$/, ';?'); // semico= lon is inserted if the function ends with a comment.replace(/\s+/g, '\\s+'); + re =3D new RegExp('function' + name + '\\s*\$\\s*' + args + '= \\s*\$\\s*{\\s*' + body + '\\s*}'); + } + + // look for a normal function definition + if ((result =3D findSourceInUrls(re, urls))) { + return result; + } + + // look for an old-school event handler function + if ((parts =3D eventRE.exec(code))) { + var event =3D parts[1]; + body =3D escapeCodeAsRegExpForMatchingInsideHTML(parts[2]); + + // look for a function defined in HTML as an onXXX handler + re =3D new RegExp('on' + event + '=3D[\\\'"]\\s*' + body + '\\= s*[\\\'"]', 'i'); + + if ((result =3D findSourceInUrls(re, urls[0]))) { + return result; + } + + // look for ??? + re =3D new RegExp(body); + + if ((result =3D findSourceInUrls(re, urls))) { + return result; + } + } + + return null; + } + + // Contents of Exception in various browsers. + // + // SAFARI: + // ex.message =3D Can't find variable: qq + // ex.line =3D 59 + // ex.sourceId =3D 580238192 + // ex.sourceURL =3D http://... + // ex.expressionBeginOffset =3D 96 + // ex.expressionCaretOffset =3D 98 + // ex.expressionEndOffset =3D 98 + // ex.name =3D ReferenceError + // + // FIREFOX: + // ex.message =3D qq is not defined + // ex.fileName =3D http://... + // ex.lineNumber =3D 59 + // ex.stack =3D ...stack trace... (see the example below) + // ex.name =3D ReferenceError + // + // CHROME: + // ex.message =3D qq is not defined + // ex.name =3D ReferenceError + // ex.type =3D not_defined + // ex.arguments =3D ['aa'] + // ex.stack =3D ...stack trace... + // + // INTERNET EXPLORER: + // ex.message =3D ... + // ex.name =3D ReferenceError + // + // OPERA: + // ex.message =3D ...message... (see the example below) + // ex.name =3D ReferenceError + // ex.opera#sourceloc =3D 11 (pretty much useless, duplicates the inf= o in ex.message) + // ex.stacktrace =3D n/a; see 'opera:config#UserPrefs|Exceptions Have = Stacktrace' + + /** + * Computes stack trace information from the stack property. + * Chrome and Gecko use this property. + * @param {Error} ex + * @return {?Object.<string, *>} Stack trace information. + */ + function computeStackTraceFromStackProp(ex) { + if (!ex.stack) { + return null; + } + + var chrome =3D /^\s*at (?:((?:\[object object\])?\S+) )?$?((?:fil= e|http|https):.*?):(\d+)(?::(\d+))?$?\s*$/i, + gecko =3D /^\s*(\S*)(?:$(.*?)$)?@((?:file|http|https).*?):(\= d+)(?::(\d+))?\s*$/i, + lines =3D ex.stack.split('\n'), + stack =3D [], + parts, + element, + reference =3D /^(.*) is undefined$/.exec(ex.message); + + for (var i =3D 0, j =3D lines.length; i < j; ++i) { + if ((parts =3D gecko.exec(lines[i]))) { + element =3D { + 'url': parts[3], + 'func': parts[1] || '?', + 'args': parts[2] ? parts[2].split(',') : '', + 'line': +parts[4], + 'column': parts[5] ? +parts[5] : null + }; + } else if ((parts =3D chrome.exec(lines[i]))) { + element =3D { + 'url': parts[2], + 'func': parts[1] || '?', + 'line': +parts[3], + 'column': parts[4] ? +parts[4] : null + }; + } else { + continue; + } + + if (!element.func && element.line) { + element.func =3D guessFunctionName(element.url, element.li= ne); + } + + if (element.line) { + element.context =3D gatherContext(element.url, element.lin= e); + } + + stack.push(element); + } + + if (stack[0] && stack[0].line && !stack[0].column && reference) { + stack[0].column =3D findSourceInLine(reference[1], stack[0].ur= l, stack[0].line); + } + + if (!stack.length) { + return null; + } + + return { + 'mode': 'stack', + 'name': ex.name, + 'message': ex.message, + 'url': document.location.href, + 'stack': stack, + 'useragent': navigator.userAgent + }; + } + + /** + * Computes stack trace information from the stacktrace property. + * Opera 10 uses this property. + * @param {Error} ex + * @return {?Object.<string, *>} Stack trace information. + */ + function computeStackTraceFromStacktraceProp(ex) { + // Access and store the stacktrace property before doing ANYTHING + // else to it because Opera is not very good at providing it + // reliably in other circumstances. + var stacktrace =3D ex.stacktrace; + + var testRE =3D / line (\d+), column (\d+) in (?:<anonymous functio= n: ([^>]+)>|([^\)]+))$(.*)$ in (.*):\s*$/i, + lines =3D stacktrace.split('\n'), + stack =3D [], + parts; + + for (var i =3D 0, j =3D lines.length; i < j; i +=3D 2) { + if ((parts =3D testRE.exec(lines[i]))) { + var element =3D { + 'line': +parts[1], + 'column': +parts[2], + 'func': parts[3] || parts[4], + 'args': parts[5] ? parts[5].split(',') : [], + 'url': parts[6] + }; + + if (!element.func && element.line) { + element.func =3D guessFunctionName(element.url, elemen= t.line); + } + if (element.line) { + try { + element.context =3D gatherContext(element.url, ele= ment.line); + } catch (exc) {} + } + + if (!element.context) { + element.context =3D [lines[i + 1]]; + } + + stack.push(element); + } + } + + if (!stack.length) { + return null; + } + + return { + 'mode': 'stacktrace', + 'name': ex.name, + 'message': ex.message, + 'url': document.location.href, + 'stack': stack, + 'useragent': navigator.userAgent + }; + } + + /** + * NOT TESTED. + * Computes stack trace information from an error message that includes + * the stack trace. + * Opera 9 and earlier use this method if the option to show stack + * traces is turned on in opera:config. + * @param {Error} ex + * @return {?Object.<string, *>} Stack information. + */ + function computeStackTraceFromOperaMultiLineMessage(ex) { + // Opera includes a stack trace into the exception message. An exa= mple is: + // + // Statement on line 3: Undefined variable: undefinedFunc + // Backtrace: + // Line 3 of linked script file://localhost/Users/andreyvit/Proj= ects/TraceKit/javascript-client/sample.js: In function zzz + // undefinedFunc(a); + // Line 7 of inline#1 script in file://localhost/Users/andreyvit= /Projects/TraceKit/javascript-client/sample.html: In function yyy + // zzz(x, y, z); + // Line 3 of inline#1 script in file://localhost/Users/andreyvit= /Projects/TraceKit/javascript-client/sample.html: In function xxx + // yyy(a, a, a); + // Line 1 of function script + // try { xxx('hi'); return false; } catch(ex) { TraceKit.repor= t(ex); } + // ... + + var lines =3D ex.message.split('\n'); + if (lines.length < 4) { + return null; + } + + var lineRE1 =3D /^\s*Line (\d+) of linked script ((?:file|http|htt= ps)\S+)(?:: in function (\S+))?\s*$/i, + lineRE2 =3D /^\s*Line (\d+) of inline#(\d+) script in ((?:file= |http|https)\S+)(?:: in function (\S+))?\s*$/i, + lineRE3 =3D /^\s*Line (\d+) of function script\s*$/i, + stack =3D [], + scripts =3D document.getElementsByTagName('script'), + inlineScriptBlocks =3D [], + parts, + i, + len, + source; + + for (i in scripts) { + if (TraceKit._has(scripts, i) && !scripts[i].src) { + inlineScriptBlocks.push(scripts[i]); + } + } + + for (i =3D 2, len =3D lines.length; i < len; i +=3D 2) { + var item =3D null; + if ((parts =3D lineRE1.exec(lines[i]))) { + item =3D { + 'url': parts[2], + 'func': parts[3], + 'line': +parts[1] + }; + } else if ((parts =3D lineRE2.exec(lines[i]))) { + item =3D { + 'url': parts[3], + 'func': parts[4] + }; + var relativeLine =3D (+parts[1]); // relative to the start= of the <SCRIPT> block + var script =3D inlineScriptBlocks[parts[2] - 1]; + if (script) { + source =3D getSource(item.url); + if (source) { + source =3D source.join('\n'); + var pos =3D source.indexOf(script.innerText); + if (pos >=3D 0) { + item.line =3D relativeLine + source.substring(= 0, pos).split('\n').length; + } + } + } + } else if ((parts =3D lineRE3.exec(lines[i]))) { + var url =3D window.location.href.replace(/#.*$/, ''), + line =3D parts[1]; + var re =3D new RegExp(escapeCodeAsRegExpForMatchingInsideH= TML(lines[i + 1])); + source =3D findSourceInUrls(re, [url]); + item =3D { + 'url': url, + 'line': source ? source.line : line, + 'func': '' + }; + } + + if (item) { + if (!item.func) { + item.func =3D guessFunctionName(item.url, item.line); + } + var context =3D gatherContext(item.url, item.line); + var midline =3D (context ? context[Math.floor(context.leng= th / 2)] : null); + if (context && midline.replace(/^\s*/, '') =3D=3D=3D lines= [i + 1].replace(/^\s*/, '')) { + item.context =3D context; + } else { + // if (context) alert("Context mismatch. Correct midli= ne:\n" + lines[i+1] + "\n\nMidline:\n" + midline + "\n\nContext:\n" + conte= xt.join("\n") + "\n\nURL:\n" + item.url); + item.context =3D [lines[i + 1]]; + } + stack.push(item); + } + } + if (!stack.length) { + return null; // could not parse multiline exception message as= Opera stack trace + } + + return { + 'mode': 'multiline', + 'name': ex.name, + 'message': lines[0], + 'url': document.location.href, + 'stack': stack, + 'useragent': navigator.userAgent + }; + } + + /** + * Adds information about the first frame to incomplete stack traces. + * Safari and IE require this to get complete data on the first frame. + * @param {Object.<string, *>} stackInfo Stack trace information from + * one of the compute* methods. + * @param {string} url The URL of the script that caused an error. + * @param {(number|string)} lineNo The line number of the script that + * caused an error. + * @param {string=3D} message The error generated by the browser, which + * hopefully contains the name of the object that caused the error. + * @return {boolean} Whether or not the stack information was + * augmented. + */ + function augmentStackTraceWithInitialElement(stackInfo, url, lineNo, m= essage) { + var initial =3D { + 'url': url, + 'line': lineNo + }; + + if (initial.url && initial.line) { + stackInfo.incomplete =3D false; + + if (!initial.func) { + initial.func =3D guessFunctionName(initial.url, initial.li= ne); + } + + if (!initial.context) { + initial.context =3D gatherContext(initial.url, initial.lin= e); + } + + var reference =3D / '([^']+)' /.exec(message); + if (reference) { + initial.column =3D findSourceInLine(reference[1], initial.= url, initial.line); + } + + if (stackInfo.stack.length > 0) { + if (stackInfo.stack[0].url =3D=3D=3D initial.url) { + if (stackInfo.stack[0].line =3D=3D=3D initial.line) { + return false; // already in stack trace + } else if (!stackInfo.stack[0].line && stackInfo.stack= [0].func =3D=3D=3D initial.func) { + stackInfo.stack[0].line =3D initial.line; + stackInfo.stack[0].context =3D initial.context; + return false; + } + } + } + + stackInfo.stack.unshift(initial); + stackInfo.partial =3D true; + return true; + } else { + stackInfo.incomplete =3D true; + } + + return false; + } + + /** + * Computes stack trace information by walking the arguments.caller + * chain at the time the exception occurred. This will cause earlier + * frames to be missed but is the only way to get any stack trace in + * Safari and IE. The top frame is restored by + * {@link augmentStackTraceWithInitialElement}. + * @param {Error} ex + * @return {?Object.<string, *>} Stack trace information. + */ + function computeStackTraceByWalkingCallerChain(ex, depth) { + var functionName =3D /function\s+([_$a-zA-Z\xA0-\uFFFF][_$a-zA-Z0-= 9\xA0-\uFFFF]*)?\s*\(/i, + stack =3D [], + funcs =3D {}, + recursion =3D false, + parts, + item, + source; + + for (var curr =3D computeStackTraceByWalkingCallerChain.caller; cu= rr && !recursion; curr =3D curr.caller) { + if (curr =3D=3D=3D computeStackTrace || curr =3D=3D=3D TraceKi= t.report) { + // console.log('skipping internal function'); + continue; + } + + item =3D { + 'url': null, + 'func': '?', + 'line': null, + 'column': null + }; + + if (curr.name) { + item.func =3D curr.name; + } else if ((parts =3D functionName.exec(curr.toString()))) { + item.func =3D parts[1]; + } + + if ((source =3D findSourceByFunctionBody(curr))) { + item.url =3D source.url; + item.line =3D source.line; + + if (item.func =3D=3D=3D '?') { + item.func =3D guessFunctionName(item.url, item.line); + } + + var reference =3D / '([^']+)' /.exec(ex.message || ex.desc= ription); + if (reference) { + item.column =3D findSourceInLine(reference[1], source.= url, source.line); + } + } + + if (funcs['' + curr]) { + recursion =3D true; + }else{ + funcs['' + curr] =3D true; + } + + stack.push(item); + } + + if (depth) { + // console.log('depth is ' + depth); + // console.log('stack is ' + stack.length); + stack.splice(0, depth); + } + + var result =3D { + 'mode': 'callers', + 'name': ex.name, + 'message': ex.message, + 'url': document.location.href, + 'stack': stack, + 'useragent': navigator.userAgent + }; + augmentStackTraceWithInitialElement(result, ex.sourceURL || ex.fil= eName, ex.line || ex.lineNumber, ex.message || ex.description); + return result; + } + + /** + * Computes a stack trace for an exception. + * @param {Error} ex + * @param {(string|number)=3D} depth + */ + function computeStackTrace(ex, depth) { + var stack =3D null; + depth =3D (depth =3D=3D null ? 0 : +depth); + + try { + // This must be tried first because Opera 10 *destroys* + // its stacktrace property if you try to access the stack + // property first!! + stack =3D computeStackTraceFromStacktraceProp(ex); + if (stack) { + return stack; + } + } catch (e) { + if (debug) { + throw e; + } + } + + try { + stack =3D computeStackTraceFromStackProp(ex); + if (stack) { + return stack; + } + } catch (e) { + if (debug) { + throw e; + } + } + + try { + stack =3D computeStackTraceFromOperaMultiLineMessage(ex); + if (stack) { + return stack; + } + } catch (e) { + if (debug) { + throw e; + } + } + + try { + stack =3D computeStackTraceByWalkingCallerChain(ex, depth + 1); + if (stack) { + return stack; + } + } catch (e) { + if (debug) { + throw e; + } + } + + return { + 'mode': 'failed' + }; + } + + /** + * Logs a stacktrace starting from the previous call and working down. + * @param {(number|string)=3D} depth How many frames deep to trace. + * @return {Object.<string, *>} Stack trace information. + */ + function computeStackTraceOfCaller(depth) { + depth =3D (depth =3D=3D null ? 0 : +depth) + 1; // "+ 1" because "= ofCaller" should drop one frame + try { + throw new Error(); + } catch (ex) { + return computeStackTrace(ex, depth + 1); + } + + return null; + } + + computeStackTrace.augmentStackTraceWithInitialElement =3D augmentStack= TraceWithInitialElement; + computeStackTrace.guessFunctionName =3D guessFunctionName; + computeStackTrace.gatherContext =3D gatherContext; + computeStackTrace.ofCaller =3D computeStackTraceOfCaller; + + return computeStackTrace; +}()); + +/** + * Extends support for global error handling for asynchronous browser + * functions. 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a/templates/base.mako +++ b/templates/base.mako @@ -24,6 +24,17 @@ ## Default javascripts <%def name=3D"javascripts()"> =20 + ## Send errors to Sntry server if configured + %if app.config.sentry_dsn: + ${h.js( "libs/tracekit", "libs/raven" )} + <script> + Raven.config('${app.config.sentry_dsn_public}').install(); + %if trans.user: + Raven.setUser( { email: "${trans.user.email}" } ); + %endif + </script> + %endif + ${h.js( "libs/jquery/jquery", "libs/jquery/select2", @@ -54,7 +65,7 @@ error : function(){}, assert : function(){} }; - =20 + // Set up needed paths. var galaxy_paths =3D new GalaxyPaths({ root_path: '${h.url_for( "/" )}', diff -r 7950ce95b2769f2fb63bfc8a549ee9bc9fdcbed2 -r 708d0ccee63fc75eb88e5dc= 3a9e0d6d3e5ff72e7 templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -45,9 +45,18 @@ =20 ## Default javascripts <%def name=3D"javascripts()"> -  + + ## Send errors to Sntry server if configured + %if app.config.sentry_dsn: + ${h.js( "libs/tracekit", "libs/raven" )} + <script> + Raven.config('${app.config.sentry_dsn_public}').install(); + %if trans.user: + Raven.setUser( { email: "${trans.user.email}" } ); + %endif + </script> + %endif + ${h.js( 'libs/jquery/jquery', 'libs/json2', diff -r 7950ce95b2769f2fb63bfc8a549ee9bc9fdcbed2 -r 708d0ccee63fc75eb88e5dc= 3a9e0d6d3e5ff72e7 templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -74,7 +74,7 @@ }); */ =20 - $( '.tooltip' ).tooltip(); + $( '.tooltip' ).tooltip().foasdasdasdoo(); =20 // TODO: is this necessary? $( "a[minsizehint]" ).click( function() { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: james_taylor: jobs: Fix LWR after merge (merged backwards?)
by Bitbucket 02 Feb '13

02 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7950ce95b276/ changeset: 7950ce95b276 user: james_taylor date: 2013-02-02 22:37:28 summary: jobs: Fix LWR after merge (merged backwards?) affected #: 1 file diff -r fa1a29005dcaf5e3146f063f0bdc1fea36a7549c -r 7950ce95b2769f2fb63bfc8a549ee9bc9fdcbed2 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -41,227 +41,7 @@ return None return job_state - job_config = client.setup() - - self.new_working_directory = job_config['working_directory'] - self.new_outputs_directory = job_config['outputs_directory'] - self.remote_path_separator = job_config['path_separator'] - - self.__initialize_referenced_tool_files() - self.__upload_tool_files() - self.__upload_input_files() - self.__initialize_output_file_renames() - self.__initialize_config_file_renames() - self.__rewrite_and_upload_config_files() - self.__rewrite_command_line() - - def __initialize_referenced_tool_files(self): - pattern = r"(%s%s\S+)" % (self.tool_dir, os.sep) - referenced_tool_files = [] - referenced_tool_files += re.findall(pattern, self.command_line) - if self.config_files != None: - for config_file in self.config_files: - referenced_tool_files += re.findall(pattern, self.__read(config_file)) - self.referenced_tool_files = referenced_tool_files - - def __upload_tool_files(self): - for referenced_tool_file in self.referenced_tool_files: - tool_upload_response = self.client.upload_tool_file(referenced_tool_file) - self.file_renames[referenced_tool_file] = tool_upload_response['path'] - - def __upload_input_files(self): - for input_file in self.input_files: - input_upload_response = self.client.upload_input(input_file) - self.file_renames[input_file] = input_upload_response['path'] - - def __initialize_output_file_renames(self): - for output_file in self.output_files: - self.file_renames[output_file] = r'%s%s%s' % (self.new_outputs_directory, - self.remote_path_separator, - os.path.basename(output_file)) - - def __initialize_config_file_renames(self): - for config_file in self.config_files: - self.file_renames[config_file] = r'%s%s%s' % (self.new_working_directory, - self.remote_path_separator, - os.path.basename(config_file)) - - def __rewrite_paths(self, contents): - new_contents = contents - for local_path, remote_path in self.file_renames.iteritems(): - new_contents = new_contents.replace(local_path, remote_path) - return new_contents - - def __rewrite_and_upload_config_files(self): - for config_file in self.config_files: - config_contents = self.__read(config_file) - new_config_contents = self.__rewrite_paths(config_contents) - self.client.upload_config_file(config_file, new_config_contents) - - def __rewrite_command_line(self): - self.rewritten_command_line = self.__rewrite_paths(self.command_line) - - def get_rewritten_command_line(self): - return self.rewritten_command_line - - def __read(self, path): - input = open(path, "r") - try: - return input.read() - finally: - input.close() - - - -class Client(object): - """ - """ - """ - """ - def __init__(self, remote_host, job_id, private_key=None): - if not remote_host.endswith("/"): - remote_host = remote_host + "/" - ## If we don't have an explicit private_key defined, check for - ## one embedded in the URL. A URL of the form - ## https://moo@cow:8913 will try to contact https://cow:8913 - ## with a private key of moo - private_key_format = "https?://(.*)@.*/?" - private_key_match= re.match(private_key_format, remote_host) - if not private_key and private_key_match: - private_key = private_key_match.group(1) - remote_host = remote_host.replace("%s@" % private_key, '', 1) - self.remote_host = remote_host - self.job_id = job_id - self.private_key = private_key - - def url_open(self, request, data): - return urllib2.urlopen(request, data) - - def __build_url(self, command, args): - if self.private_key: - args["private_key"] = self.private_key - data = urllib.urlencode(args) - url = self.remote_host + command + "?" + data - return url - - def __raw_execute(self, command, args = {}, data = None): - url = self.__build_url(command, args) - request = urllib2.Request(url=url, data=data) - response = self.url_open(request, data) - return response - - def __raw_execute_and_parse(self, command, args = {}, data = None): - response = self.__raw_execute(command, args, data) - return simplejson.loads(response.read()) - - def __upload_file(self, action, path, contents = None): - """ """ - input = open(path, 'rb') - try: - mmapped_input = mmap.mmap(input.fileno(), 0, access = mmap.ACCESS_READ) - return self.__upload_contents(action, path, mmapped_input) - finally: - input.close() - - def __upload_contents(self, action, path, contents): - name = os.path.basename(path) - args = {"job_id" : self.job_id, "name" : name} - return self.__raw_execute_and_parse(action, args, contents) - - def upload_tool_file(self, path): - return self.__upload_file("upload_tool_file", path) - - def upload_input(self, path): - return self.__upload_file("upload_input", path) - - def upload_config_file(self, path, contents): - return self.__upload_contents("upload_config_file", path, contents) - - def download_output(self, path): - """ """ - name = os.path.basename(path) - response = self.__raw_execute('download_output', {'name' : name, - "job_id" : self.job_id}) - output = open(path, 'wb') - try: - while True: - buffer = response.read(1024) - if buffer == "": - break - output.write(buffer) - finally: - output.close() - - def launch(self, command_line): - """ """ - return self.__raw_execute("launch", {"command_line" : command_line, - "job_id" : self.job_id}) - - def kill(self): - return self.__raw_execute("kill", {"job_id" : self.job_id}) - - def wait(self): - """ """ - while True: - check_complete_response = self.__raw_execute_and_parse("check_complete", {"job_id" : self.job_id }) - complete = check_complete_response["complete"] == "true" - if complete: - return check_complete_response - time.sleep(1) - - def clean(self): - self.__raw_execute("clean", { "job_id" : self.job_id }) - - def setup(self): - return self.__raw_execute_and_parse("setup", { "job_id" : self.job_id }) - - - -class LwrJobRunner( BaseJobRunner ): - """ - Lwr Job Runner - """ - STOP_SIGNAL = object() - def __init__( self, app ): - """Start the job runner with 'nworkers' worker threads""" - self.app = app - self.sa_session = app.model.context - - # start workers - self.queue = Queue() - self.threads = [] - nworkers = app.config.local_job_queue_workers - log.info( "starting workers" ) - for i in range( nworkers ): - worker = threading.Thread( name=( "LwrJobRunner.thread-%d" % i ), target=self.run_next ) - worker.setDaemon( True ) - worker.start() - self.threads.append( worker ) - log.debug( "%d workers ready", nworkers ) - - def run_next( self ): - """Run the next job, waiting until one is available if neccesary""" - while 1: - job_wrapper = self.queue.get() - if job_wrapper is self.STOP_SIGNAL: - return - try: - self.run_job( job_wrapper ) - except: - log.exception( "Uncaught exception running job" ) - - def determine_lwr_url(self, url): - lwr_url = url[ len( 'lwr://' ) : ] - return lwr_url - - def get_client_from_wrapper(self, job_wrapper): - return self.get_client( job_wrapper.get_job_runner_url(), job_wrapper.job_id ) - - def get_client(self, job_runner, job_id): - lwr_url = self.determine_lwr_url( job_runner ) - return Client(lwr_url, job_id) - - def run_job( self, job_wrapper ): + def queue_job(self, job_wrapper): stderr = stdout = command_line = '' runner_url = job_wrapper.get_job_runner_url() @@ -458,4 +238,4 @@ elif job.get_state() == model.Job.states.QUEUED: # LWR doesn't queue currently, so this indicates galaxy was shutoff while # job was being staged. Not sure how to recover from that. - job_state.job_wrapper.fail( "This job was killed when Galaxy was restarted. Please retry the job." ) + job_state.job_wrapper.fail( "This job was killed when Galaxy was restarted. Please retry the job." ) \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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