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[hg] galaxy 1668: Rename gbrowse_elegans to wormbase_test, add a...
by Greg Von Kuster 15 Dec '08

15 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/87a9cf297998 changeset: 1668:87a9cf297998 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Dec 15 10:37:39 2008 -0500 description: Rename gbrowse_elegans to wormbase_test, add a config for the wormbase production server. 4 file(s) affected in this change: tool_conf.xml.sample tools/data_source/gbrowse_elegans.xml tools/data_source/wormbase.xml tools/data_source/wormbase_test.xml diffs (104 lines): diff -r 3a0b07161c1a -r 87a9cf297998 tool_conf.xml.sample --- a/tool_conf.xml.sample Mon Dec 15 09:06:11 2008 -0500 +++ b/tool_conf.xml.sample Mon Dec 15 10:37:39 2008 -0500 @@ -9,7 +9,8 @@ <tool file="data_source/microbial_import.xml" /> <tool file="data_source/biomart.xml" /> <tool file="data_source/biomart_test.xml" /> - <tool file="data_source/gbrowse_elegans.xml" /> + <tool file="data_source/wormbase.xml" /> + <tool file="data_source/wormbase_test.xml" /> <tool file="data_source/flymine.xml" /> <tool file="data_source/encode_db.xml" /> <tool file="data_source/epigraph_import.xml" /> diff -r 3a0b07161c1a -r 87a9cf297998 tools/data_source/gbrowse_elegans.xml --- a/tools/data_source/gbrowse_elegans.xml Mon Dec 15 09:06:11 2008 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -<?xml version="1.0"?> -<tool name="C. Elegans" id="gbrowse_elegans" tool_type="data_source" URL_method="get"> - <description>server</description> - <command interpreter="python">data_source.py $output</command> - <inputs action="http://dev.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" method="get" target="_top"> - <display>go to C. Elegans server $GALAXY_URL</display> - <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=gbrowse_elegans" /> - </inputs> - <request_param_translation> - <request_param galaxy_name="URL" remote_name="URL" missing=""> - <add_to_url> - <param_from_source name="d" missing="" /> - <param_from_source name="dbkey" missing="" /> - <param_from_source name="q" missing="" /> - <param_from_source name="s" missing="" /> - <param_from_source name="t" missing="" /> - </add_to_url> - </request_param> - <request_param galaxy_name="data_type" remote_name="data_type" missing="gff3" /> - </request_param_translation> - <uihints minwidth="800"/> - <outputs> - <data name="output" format="txt" /> - </outputs> - <options sanitize="False" refresh="True"/> -</tool> - diff -r 3a0b07161c1a -r 87a9cf297998 tools/data_source/wormbase.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/wormbase.xml Mon Dec 15 10:37:39 2008 -0500 @@ -0,0 +1,26 @@ +<?xml version="1.0"?> +<tool name="Wormbase" id="wormbase" tool_type="data_source" URL_method="get"> + <description>server</description> + <command interpreter="python">data_source.py $output</command> + <inputs action="http://www.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" method="get" target="_top"> + <display>go to Wormbase server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=wormbase" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL" remote_name="URL" missing=""> + <add_to_url> + <param_from_source name="d" missing="" /> + <param_from_source name="dbkey" missing="" /> + <param_from_source name="q" missing="" /> + <param_from_source name="s" missing="" /> + <param_from_source name="t" missing="" /> + </add_to_url> + </request_param> + <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" /> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> diff -r 3a0b07161c1a -r 87a9cf297998 tools/data_source/wormbase_test.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/wormbase_test.xml Mon Dec 15 10:37:39 2008 -0500 @@ -0,0 +1,26 @@ +<?xml version="1.0"?> +<tool name="Wormbase" id="wormbase_test" tool_type="data_source" URL_method="get"> + <description>test server</description> + <command interpreter="python">data_source.py $output</command> + <inputs action="http://dev.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" method="get" target="_top"> + <display>go to Wormbase test server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=wormbase_test" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL" remote_name="URL" missing=""> + <add_to_url> + <param_from_source name="d" missing="" /> + <param_from_source name="dbkey" missing="" /> + <param_from_source name="q" missing="" /> + <param_from_source name="s" missing="" /> + <param_from_source name="t" missing="" /> + </add_to_url> + </request_param> + <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" /> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool>

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[hg] galaxy 1664: Add ability for data_source tools to append pa...
by Greg Von Kuster 14 Dec '08

14 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/5f4511a5b4d6 changeset: 1664:5f4511a5b4d6 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Sat Dec 13 23:35:29 2008 -0500 description: Add ability for data_source tools to append parameters passed in the initial response to the value of URL prior to Galaxy's post to the URL. This is a cleaner method for Biomart and also gets GBrowse to wrok. 8 file(s) affected in this change: lib/galaxy/tools/__init__.py lib/galaxy/util/__init__.py tools/data_source/biomart.xml tools/data_source/biomart_test.xml tools/data_source/data_source.py tools/data_source/gbrowse_datasource.py tools/data_source/gbrowse_elegans.xml tools/data_source/gbrowse_filter_code.py diffs (293 lines): diff -r 0af3897ce585 -r 5f4511a5b4d6 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Fri Dec 12 14:33:51 2008 -0500 +++ b/lib/galaxy/tools/__init__.py Sat Dec 13 23:35:29 2008 -0500 @@ -231,8 +231,6 @@ # data_source tool if self.tool_type == "data_source": self.URL_method = root.get( "URL_method", "get" ) # get is the default - # TODO: Biomart hack - eliminate when they encode URL - they'll let us know when... - self.add_to_URL = root.get( "add_to_URL", None ) self.param_trans_dict = {} req_param_trans = root.find( "request_param_translation" ) if req_param_trans is not None: @@ -255,6 +253,22 @@ galaxy_format = format.get( "galaxy_format" ) format_trans_dict[ remote_format ] = galaxy_format trans_list.append( format_trans_dict ) + elif req_param.get( "galaxy_name" ) == "URL": + # Some remote data sources ( e.g., Gbrowse ) send parameters back to + # Galaxy in the initial response that must be added to URL prior to + # Galaxy sending the secondary request to the URL. The tag set looks + # asomething like: + # <add_to_url> + # <param_from_source name="d" missing="" /> + # </add_to_url> + add_to_url = req_param.find( "add_to_url" ) + if add_to_url is not None: + add_to_url_dict = {} + for param_from_source in add_to_url.findall( "param_from_source" ): + name = param_from_source.get( "name" ) + value = param_from_source.get( "missing" ) # only used if the source doesn't send the param name + add_to_url_dict[ name ] = value + trans_list.append( add_to_url_dict ) self.param_trans_dict[ remote_name ] = trans_list # Command line (template). Optional for tools that do not invoke a local program command = root.find("command") @@ -1162,11 +1176,16 @@ description = param_dict.get( 'position', '' ) if not description: description = 'unknown position' + gb_landmark_region = param_dict.get( 'q' ) data_type = param_dict.get( 'data_type' ) items = out_data.items() for name, data in items: if organism and table and description: + # This is UCSC data.name = '%s on %s: %s (%s)' % ( data.name, organism, table, description ) + elif gb_landmark_region: + # This is GBrowse + data.name = '%s on %s' % ( data.name, gb_landmark_region ) data.info = info data.dbkey = dbkey try: diff -r 0af3897ce585 -r 5f4511a5b4d6 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py Fri Dec 12 14:33:51 2008 -0500 +++ b/lib/galaxy/util/__init__.py Sat Dec 13 23:35:29 2008 -0500 @@ -159,10 +159,31 @@ try: # The Galaxy "data_type entry is special in that it can include the ability # to translate the format to a Galaxy supported format. In the dict, this entry - # looks something like: {'hgta_outputType': ['data_type', 'bed', {'selectedFields': 'tabular'}] } + # looks something like: + # {'hgta_outputType': ['data_type', 'bed', {'selectedFields': 'tabular'}] } format_trans_dict = tool.param_trans_dict[ key ][2] if value in format_trans_dict: new_value = format_trans_dict[ value ] + except: + pass + elif new_key == 'URL': + # As above, the URL can include a set of params from the remote data source + # that must be appended to the URL prior to the post. In this case, the + # dict entry would look something like: + # ['URL', '', {'q': '', 's': '', 'd': '', 'dbkey': '', 't': ''}] + try: + add_to_url_dict = tool.param_trans_dict[ key ][2] + if new_value.count( '?' ) == 0: + sep = '?' + else: + sep = '&' + for param_name, missing_value in add_to_url_dict.items(): + param_value = params.get( param_name, None ) + if not param_value and missing_value: + param_value = missing_value + if param_value: + new_value += '%s%s=%s' % ( sep, param_name, param_value ) + sep = '&' except: pass if not value and not new_value: @@ -174,9 +195,6 @@ if tool and tool.tool_type == 'data_source': # Add the tool's URL_method to params self.__dict__[ 'URL_method' ] = tool.URL_method - # TODO: Biomart hack - eliminate when they encode URL - they'll let us know when... - if tool.add_to_URL is not None: - self.__dict__[ 'add_to_URL' ] = tool.add_to_URL for key, value in tool.param_trans_dict.items(): # Make sure that all translated values used in Galaxy are added to the params galaxy_name = tool.param_trans_dict[ key ][0] diff -r 0af3897ce585 -r 5f4511a5b4d6 tools/data_source/biomart.xml --- a/tools/data_source/biomart.xml Fri Dec 12 14:33:51 2008 -0500 +++ b/tools/data_source/biomart.xml Sat Dec 13 23:35:29 2008 -0500 @@ -7,7 +7,7 @@ TODO: Hack to get biomart to work - the 'add_to_URL' param can be eliminated when the Biomart team encodes URL prior to sending, meanwhile everything including and beyond the first '&' is truncated from URL. They said they'll let us know when this is fixed at their end. --> -<tool name="BioMart" id="biomart" tool_type="data_source" URL_method="get" add_to_URL="biomart_hack"> +<tool name="BioMart" id="biomart" tool_type="data_source" URL_method="get"> <description>Central server</description> <command interpreter="python">data_source.py $output</command> <inputs action="http://www.biomart.org/biomart/martview" check_values="false" method="get" target="_top"> @@ -15,7 +15,12 @@ <param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" /> </inputs> <request_param_translation> - <request_param galaxy_name="URL" remote_name="URL" missing="" /> + <request_param galaxy_name="URL" remote_name="URL" missing=""> + <add_to_url> + <param_from_source name="_export" missing="1" /> + <param_from_source name="GALAXY_URL" missing="0" /> + </add_to_url> + </request_param> <request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" /> <request_param galaxy_name="organism" remote_name="organism" missing="" /> <request_param galaxy_name="table" remote_name="table" missing="" /> diff -r 0af3897ce585 -r 5f4511a5b4d6 tools/data_source/biomart_test.xml --- a/tools/data_source/biomart_test.xml Fri Dec 12 14:33:51 2008 -0500 +++ b/tools/data_source/biomart_test.xml Sat Dec 13 23:35:29 2008 -0500 @@ -7,7 +7,7 @@ TODO: Hack to get biomart to work - the 'add_to_URL' param can be eliminated when the Biomart team encodes URL prior to sending, meanwhile everything including and beyond the first '&' is truncated from URL. They said they'll let us know when this is fixed at their end. --> -<tool name="BioMart" id="biomart_test" tool_type="data_source" URL_method="get" add_to_URL="biomart_hack"> +<tool name="BioMart" id="biomart_test" tool_type="data_source" URL_method="get"> <description>Test server</description> <command interpreter="python">data_source.py $output</command> <inputs action="http://test.biomart.org/biomart/martview" check_values="false" method="get" target="_top"> @@ -15,7 +15,12 @@ <param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" /> </inputs> <request_param_translation> - <request_param galaxy_name="URL" remote_name="URL" missing="" /> + <request_param galaxy_name="URL" remote_name="URL" missing=""> + <add_to_url> + <param_from_source name="_export" missing="1" /> + <param_from_source name="GALAXY_URL" missing="0" /> + </add_to_url> + </request_param> <request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" /> <request_param galaxy_name="organism" remote_name="organism" missing="" /> <request_param galaxy_name="table" remote_name="table" missing="" /> diff -r 0af3897ce585 -r 5f4511a5b4d6 tools/data_source/data_source.py --- a/tools/data_source/data_source.py Fri Dec 12 14:33:51 2008 -0500 +++ b/tools/data_source/data_source.py Sat Dec 13 23:35:29 2008 -0500 @@ -33,12 +33,6 @@ if not URL: open( filename, 'w' ).write( "" ) stop_err( 'The remote data source application has not sent back a URL parameter in the request.' ) - # TODO: Hack to get biomart to work - this can be eliminated when the Biomart team encodes URL prior to sending, meanwhile - # everything including and beyond the first '&' is truncated from URL. They said they'll let us know when this is fixed - # at their end. - add_to_URL = params.get( 'add_to_URL', None ) - if add_to_URL: - URL += '&_export=1&GALAXY_URL=0' URL_method = params.get( 'URL_method', None ) out = open( filename, 'w' ) CHUNK_SIZE = 2**20 # 1Mb diff -r 0af3897ce585 -r 5f4511a5b4d6 tools/data_source/gbrowse_datasource.py --- a/tools/data_source/gbrowse_datasource.py Fri Dec 12 14:33:51 2008 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ -#!/usr/bin/env python -#Retreives data from GMOD and stores in a file. GBrowse parameters are provided in the input/output file. -import urllib, sys, os, gzip, tempfile, shutil -from galaxy import eggs -from galaxy.datatypes import data - -assert sys.version_info[:2] >= ( 2, 4 ) - -def stop_err( msg ): - sys.stderr.write( msg ) - sys.exit() - -def __main__(): - filename = sys.argv[1] - params = {} - - for line in open( filename, 'r' ): - try: - line = line.strip() - fields = line.split( '\t' ) - params[ fields[0] ] = fields[1] - except: - continue - - URL = params.get( 'URL', None ) - if not URL: - open( filename, 'w' ).write( "" ) - stop_err( 'Datasource has not sent back a URL parameter.' ) - - for i, param in enumerate( params.keys() ): - if i == 0: - sep = '?' - else: - sep = '&' - if param != '__collected_datasets__': - URL += "%s%s=%s" % ( sep, param, params.get( param ) ) - - CHUNK_SIZE = 2**20 # 1Mb - try: - page = urllib.urlopen( URL ) - except Exception, exc: - raise Exception( 'Problems connecting to %s (%s)' % ( URL, exc ) ) - sys.exit( 1 ) - - fp = open( filename, 'wb' ) - while 1: - chunk = page.read( CHUNK_SIZE ) - if not chunk: - break - fp.write( chunk ) - fp.close() - -if __name__ == "__main__": __main__() diff -r 0af3897ce585 -r 5f4511a5b4d6 tools/data_source/gbrowse_elegans.xml --- a/tools/data_source/gbrowse_elegans.xml Fri Dec 12 14:33:51 2008 -0500 +++ b/tools/data_source/gbrowse_elegans.xml Sat Dec 13 23:35:29 2008 -0500 @@ -1,13 +1,24 @@ <?xml version="1.0"?> -<tool name="C. Elegans" id="gbrowse_elegans"> +<tool name="C. Elegans" id="gbrowse_elegans" tool_type="data_source" URL_method="get"> <description>server</description> - <command interpreter="python">gbrowse_datasource.py $output</command> - <inputs action="http://www.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" method="get" target="_top"> + <command interpreter="python">data_source.py $output</command> + <inputs action="http://dev.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" method="get" target="_top"> <display>go to C. Elegans server $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=gbrowse_elegans" /> </inputs> + <request_param_translation> + <request_param galaxy_name="URL" remote_name="URL" missing=""> + <add_to_url> + <param_from_source name="d" missing="" /> + <param_from_source name="dbkey" missing="" /> + <param_from_source name="q" missing="" /> + <param_from_source name="s" missing="" /> + <param_from_source name="t" missing="" /> + </add_to_url> + </request_param> + <request_param galaxy_name="data_type" remote_name="data_type" missing="gff3" /> + </request_param_translation> <uihints minwidth="800"/> - <code file="gbrowse_filter_code.py"/> <outputs> <data name="output" format="txt" /> </outputs> diff -r 0af3897ce585 -r 5f4511a5b4d6 tools/data_source/gbrowse_filter_code.py --- a/tools/data_source/gbrowse_filter_code.py Fri Dec 12 14:33:51 2008 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ -# Code for direct connection to GMOD -from galaxy.datatypes import sniff -import urllib - -import logging -log = logging.getLogger( __name__ ) - -def exec_before_job( app, inp_data, out_data, param_dict, tool=None ): - """Sets the attributes of the data""" - gb_settings = urllib.unquote( param_dict.get( 't', None ) ) # t=CG+TS+ESTB+SAGE+EXPR+EXPR_PATTERN+SNPs+PolyA+BLASTX+LINK+ETILE - gb_landmark_region = urllib.unquote( param_dict.get( 'q' ) ) # q=IV:6070000..6100000& - gb_land_mark, gb_region = gb_landmark_region.split( ':' ) - items = out_data.items() - for name, data in items: - data.name = "%s on %s" % ( data.name, gb_landmark_region ) - data.dbkey = param_dict.get( 'dbkey', '?' ) - # Store GMOD / GBrowse parameters temporarily in output file - out = open( data.file_name, 'w' ) - for key, value in param_dict.items(): - out.write( "%s\t%s\n" % ( key, value ) ) - out.close() - out_data[ name ] = data - -def exec_after_process( app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None ): - """Verifies the data after the run""" - name, data = out_data.items()[0] - data.set_size() - if data.state == data.states.OK: - data.info = data.name - if data.extension == 'txt': - data_type = sniff.guess_ext( data.file_name, sniff_order=app.datatypes_registry.sniff_order ) - data = app.datatypes_registry.change_datatype( data, data_type ) - data.set_peek() - data.flush()

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what is the status of GALAXY integration with GBrowse?
by David M. Goodstein 12 Dec '08

12 Dec '08

Specifically the ability to pull and push data to/from Galaxy to a Gbrowser? thx, --David David M. Goodstein Joint Genome Institute / Lawrence Berkeley National Lab Center for Integrative Genomics / UCBerkeley

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[hg] galaxy 1663: Fix for showing deleted datasets in a history, ...
by Greg Von Kuster 12 Dec '08

12 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/0af3897ce585 changeset: 1663:0af3897ce585 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Dec 12 14:33:51 2008 -0500 description: Fix for showing deleted datasets in a history, also yet another fix for the new users report, users are now sorted descending by last login, as the report states. 4 file(s) affected in this change: lib/galaxy/webapps/reports/controllers/users.py lib/galaxy/webapps/reports/templates/users_last_access_date.mako templates/history/options.mako templates/root/history.mako diffs (73 lines): diff -r d53da5b089a8 -r 0af3897ce585 lib/galaxy/webapps/reports/controllers/users.py --- a/lib/galaxy/webapps/reports/controllers/users.py Fri Dec 12 12:12:59 2008 -0500 +++ b/lib/galaxy/webapps/reports/controllers/users.py Fri Dec 12 14:33:51 2008 -0500 @@ -1,6 +1,6 @@ from datetime import datetime, timedelta from time import strftime -import calendar +import calendar, operator from galaxy.webapps.reports.base.controller import * import galaxy.model from galaxy.model.orm import * @@ -112,6 +112,7 @@ else: # The user has never logged in users.append( ( user.email, "never logged in" ) ) + users = sorted( users, key=operator.itemgetter( 1 ), reverse=True ) return trans.fill_template( 'users_last_access_date.mako', users=users, not_logged_in_for_days=not_logged_in_for_days, diff -r d53da5b089a8 -r 0af3897ce585 lib/galaxy/webapps/reports/templates/users_last_access_date.mako --- a/lib/galaxy/webapps/reports/templates/users_last_access_date.mako Fri Dec 12 12:12:59 2008 -0500 +++ b/lib/galaxy/webapps/reports/templates/users_last_access_date.mako Fri Dec 12 14:33:51 2008 -0500 @@ -13,7 +13,12 @@ <td> <form method="post" controller="users" action="last_access_date"> <p> - Users that have not logged in to Galaxy for + %if users: + ${len( users ) } + %else: + 0 + %endif +  users have not logged in to Galaxy for <input type="textfield" value="${not_logged_in_for_days}" size="3" name="not_logged_in_for_days"> days.  <button name="action" value="not_logged_in_for_days">Go</button> </p> diff -r d53da5b089a8 -r 0af3897ce585 templates/history/options.mako --- a/templates/history/options.mako Fri Dec 12 12:12:59 2008 -0500 +++ b/templates/history/options.mako Fri Dec 12 14:33:51 2008 -0500 @@ -11,15 +11,15 @@ <ul> %if user: - <li><a href="${h.url_for( action='history_rename', id=history.id )}" target="galaxy_main">Rename</a> current history (stored as "${history.name}")</li> - <li><a href="${h.url_for( action='history_available')}" target="galaxy_main">List</a> previously stored histories</li> + <li><a href="${h.url_for( controller='root', action='history_rename', id=history.id )}" target="galaxy_main">Rename</a> current history (stored as "${history.name}")</li> + <li><a href="${h.url_for( controller='root', action='history_available')}" target="galaxy_main">List</a> previously stored histories</li> %if len( history.active_datasets ) > 0: - <li><a href="${h.url_for('/history_new')}">Create</a> a new empty history</li> + <li><a href="${h.url_for( controller='root', action='history_new' )}">Create</a> a new empty history</li> %endif <li><a href="${h.url_for( controller='workflow', action='build_from_current_history' )}">Construct workflow</a> from the current history</li> - <li><a href="${h.url_for( action='history_share' )}" target="galaxy_main">Share</a> current history</div> + <li><a href="${h.url_for( controller='root', action='history_share' )}" target="galaxy_main">Share</a> current history</div> %endif - <li><a href="${h.url_for( action='history', show_deleted=True)}" target="galaxy_history">Show deleted</a> datasets in history</li> - <li><a href="${h.url_for( action='history_delete', id=history.id )}" confirm="Are you sure you want to delete the current history?">Delete</a> current history</div> + <li><a href="${h.url_for( controller='root', action='history', show_deleted=True)}" target="galaxy_history">Show deleted</a> datasets in history</li> + <li><a href="${h.url_for( controller='root', action='history_delete', id=history.id )}" confirm="Are you sure you want to delete the current history?">Delete</a> current history</div> </ul> diff -r d53da5b089a8 -r 0af3897ce585 templates/root/history.mako --- a/templates/root/history.mako Fri Dec 12 12:12:59 2008 -0500 +++ b/templates/root/history.mako Fri Dec 12 14:33:51 2008 -0500 @@ -248,7 +248,7 @@ <%namespace file="history_common.mako" import="render_dataset" /> -%if ( show_deleted and len( history.datasets ) < 1 ) or len( history.active_datasets ) < 1: +%if ( show_deleted and not history.activatable_datasets ) or ( not show_deleted and not history.active_datasets ): <div class="infomessagesmall" id="emptyHistoryMessage"> %else: <%

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[hg] galaxy 1662: Added more test-cases to GOPS JOIN to include ...
by Greg Von Kuster 12 Dec '08

12 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/d53da5b089a8 changeset: 1662:d53da5b089a8 user: guru date: Fri Dec 12 12:12:59 2008 -0500 description: Added more test-cases to GOPS JOIN to include cases with different cut-offs for overlap. 3 file(s) affected in this change: test-data/gops-join-both-100.dat test-data/gops-join-none-500.dat tools/new_operations/join.xml diffs (139 lines): diff -r 8e3d63d7cd8a -r d53da5b089a8 test-data/gops-join-both-100.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops-join-both-100.dat Fri Dec 12 12:12:59 2008 -0500 @@ -0,0 +1,99 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - chr1 147962192 147962580 NM_005997_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + . . . . . . +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - chr1 148078400 148078582 AJ011123_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + chr1 148185136 148185276 NM_002796_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - . . . . . . +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + . . . . . . +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + . . . . . . +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - chr12 38440094 38440321 NM_052885_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + chr13 112381694 112381953 NM_207440_cds_1_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - chr15 41486872 41487060 BX537418_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + chr15 41673708 41673857 AK223365_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - . . . . . . +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + . . . . . . +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + . . . . . . +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - . . . . . . +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + chr16 244413 244681 AK057165_cds_2_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - chr16 259268 259383 AB016929_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - chr18 23786114 23786321 NM_001792_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + chr18 59406881 59407046 NM_012397_cds_1_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - chr18 59455932 59456337 AB046400_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + . . . . . . +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - chr19 59236026 59236146 NM_198481_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + . . . . . . +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - . . . . . . +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + . . . . . . +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - . . . . . . +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + . . . . . . +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - . . . . . . +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + chr20 33513606 33513792 AF022655_cds_1_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - . . . . . . +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + . . . . . . +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + . . . . . . +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - chr21 32869641 32870022 NM_018277_cds_3_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - . . . . . . +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + . . . . . . +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - chr22 30160419 30160661 BC032941_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + . . . . . . +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - . . . . . . +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + chr5 131424298 131424460 NM_000588_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - . . . . . . +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + . . . . . . +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - . . . . . . +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - chr6 108299600 108299744 NM_007214_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + . . . . . . +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - chr6 108640045 108640151 NM_003795_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + chr6 108722976 108723115 NM_145315_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + chr7 113660517 113660685 AF467257_cds_1_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - chr7 116512159 116512389 NM_003391_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + . . . . . . +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - chr7 116945541 116945787 AF377960_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - chr8 118881131 118881317 NM_000127_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + . . . . . . +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + . . . . . . +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - . . . . . . +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + . . . . . . +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 - +. . . . . . chr7 116714099 116714152 NM_000492_cds_0_0_chr7_116714100_f 0 + +. . . . . . chr6 108594662 108594687 NM_003269_cds_0_0_chr6_108594663_f 0 + +. . . . . . chr5 131311206 131311254 AF099740_cds_11_0_chr5_131311207_r 0 - +. . . . . . chr5 131556601 131556672 BC035813_cds_0_0_chr5_131556602_r 0 - +. . . . . . chr5 131621326 131621419 BC003096_cds_0_0_chr5_131621327_f 0 + +. . . . . . chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 + +. . . . . . chr2 118288583 118288668 NM_006773_cds_0_0_chr2_118288584_f 0 + +. . . . . . chr2 118390395 118390500 BC005078_cds_0_0_chr2_118390396_r 0 - +. . . . . . chr2 220108689 220109267 AY125465_cds_0_0_chr2_220108690_f 0 + +. . . . . . chr1 147984545 147984630 BC007833_cds_0_0_chr1_147984546_f 0 + +. . . . . . chr21 32687402 32687588 NM_032910_cds_0_0_chr21_32687403_f 0 + +. . . . . . chr21 33728358 33728724 AK129657_cds_0_0_chr21_33728359_r 0 - +. . . . . . chr9 128764156 128764189 BC051300_cds_0_0_chr9_128764157_f 0 + +. . . . . . chr9 128789552 128789584 NM_015354_cds_0_0_chr9_128789553_f 0 + +. . . . . . chr9 128850516 128850624 AB058751_cds_0_0_chr9_128850517_r 0 - +. . . . . . chr13 29680676 29680875 NM_032116_cds_0_0_chr13_29680677_r 0 - +. . . . . . chr12 38905200 38905351 AY792511_cds_0_0_chr12_38905201_f 0 + +. . . . . . chr11 116124407 116124501 AK057832_cds_0_0_chr11_116124408_r 0 - +. . . . . . chr11 116206508 116206563 NM_000040_cds_1_0_chr11_116206509_f 0 + +. . . . . . chr11 130745911 130745993 AY358331_cds_0_0_chr11_130745912_f 0 + +. . . . . . chr22 30120223 30120265 NM_004147_cds_0_0_chr22_30120224_f 0 + +. . . . . . chr22 30228824 30228916 NM_001007467_cds_1_0_chr22_30228825_f 0 + +. . . . . . chr22 30340151 30340376 CR456540_cds_0_0_chr22_30340152_r 0 - +. . . . . . chr16 142908 143003 NM_005332_cds_0_0_chr16_142909_f 0 + +. . . . . . chr16 179197 179339 BC065198_cds_0_0_chr16_179198_r 0 - +. . . . . . chr15 41679161 41679250 NM_153700_cds_0_0_chr15_41679162_r 0 - +. . . . . . chr15 41773540 41773689 AK223365_cds_0_0_chr15_41773541_f 0 + +. . . . . . chr14 98521864 98521922 U88895_cds_0_0_chr14_98521865_f 0 + +. . . . . . chr20 33330413 33330423 NM_181466_cds_0_0_chr20_33330414_r 0 - +. . . . . . chr20 33485370 33486123 BC085019_cds_1_0_chr20_33485371_f 0 + +. . . . . . chr20 33488491 33489122 NM_000557_cds_1_0_chr20_33488492_r 0 - +. . . . . . chr19 59297998 59298008 NM_004542_cds_0_0_chr19_59297999_f 0 + +. . . . . . chr19 59318205 59318718 AK128544_cds_3_0_chr19_59318206_r 0 - +. . . . . . chr18 59528407 59528575 AY792326_cds_0_0_chr18_59528408_f 0 + diff -r 8e3d63d7cd8a -r d53da5b089a8 test-data/gops-join-none-500.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops-join-none-500.dat Fri Dec 12 12:12:59 2008 -0500 @@ -0,0 +1,8 @@ +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 - +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 - +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 - +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 + diff -r 8e3d63d7cd8a -r d53da5b089a8 tools/new_operations/join.xml --- a/tools/new_operations/join.xml Fri Dec 12 11:53:06 2008 -0500 +++ b/tools/new_operations/join.xml Fri Dec 12 12:12:59 2008 -0500 @@ -51,6 +51,20 @@ <param name="fill" value="both" /> <output name="output" file="gops-join-both.dat" /> </test> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2.bed" /> + <param name="min" value="500" /> + <param name="fill" value="none" /> + <output name="output" file="gops-join-none-500.dat" /> + </test> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2.bed" /> + <param name="min" value="100" /> + <param name="fill" value="both" /> + <output name="output" file="gops-join-both-100.dat" /> + </test> </tests> <help>

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[hg] galaxy 1661: Bug fix for users report controller, some user...
by Greg Von Kuster 12 Dec '08

12 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/8e3d63d7cd8a changeset: 1661:8e3d63d7cd8a user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Dec 12 11:53:06 2008 -0500 description: Bug fix for users report controller, some users may not yet have logged in. 1 file(s) affected in this change: lib/galaxy/webapps/reports/controllers/users.py diffs (20 lines): diff -r 254c86053312 -r 8e3d63d7cd8a lib/galaxy/webapps/reports/controllers/users.py --- a/lib/galaxy/webapps/reports/controllers/users.py Fri Dec 12 10:15:37 2008 -0500 +++ b/lib/galaxy/webapps/reports/controllers/users.py Fri Dec 12 11:53:06 2008 -0500 @@ -105,9 +105,13 @@ now = strftime( "%Y-%m-%d %H:%M:%S" ) users = [] for user in galaxy.model.User.query().order_by( galaxy.model.User.table.c.email ).all(): - last_galaxy_session = user.galaxy_sessions[ 0 ] - if last_galaxy_session.update_time < cutoff_time: - users.append( ( user.email, last_galaxy_session.update_time.strftime( "%Y-%m-%d" ) ) ) + if user.galaxy_sessions: + last_galaxy_session = user.galaxy_sessions[ 0 ] + if last_galaxy_session.update_time < cutoff_time: + users.append( ( user.email, last_galaxy_session.update_time.strftime( "%Y-%m-%d" ) ) ) + else: + # The user has never logged in + users.append( ( user.email, "never logged in" ) ) return trans.fill_template( 'users_last_access_date.mako', users=users, not_logged_in_for_days=not_logged_in_for_days,

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[hg] galaxy 1660: Update bx-python to r458
by Nate Coraor 12 Dec '08

12 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/254c86053312 changeset: 1660:254c86053312 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Dec 12 10:15:37 2008 -0500 description: Update bx-python to r458 1 file(s) affected in this change: eggs.ini diffs (18 lines): diff -r cf461b1d6659 -r 254c86053312 eggs.ini --- a/eggs.ini Fri Dec 12 09:43:42 2008 -0500 +++ b/eggs.ini Fri Dec 12 10:15:37 2008 -0500 @@ -55,12 +55,12 @@ MySQL_python = _5.0.67_static python_lzo = _static flup = .dev_r2311 -bx_python = _dev_r456 +bx_python = _dev_r458 nose = .dev_r101 ; source location, necessary for scrambling [source] -bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r456.tar.bz2 +bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r458.tar.bz2 Cheetah = http://voxel.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar… DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://mysql.mirrors.pair.com/Downloads/MySQL-5.0/mysql-5.0.67.tar.gz

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[hg] galaxy 1658: Update Fasta.sniff()
by Greg Von Kuster 12 Dec '08

12 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/64506c9397e4 changeset: 1658:64506c9397e4 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Dec 11 16:00:06 2008 -0500 description: Update Fasta.sniff() Rules for sniffing as True: We don't care about line length (other than empty lines). The first non-empty line must start with '>' and the Very Next line.strip() must have sequence data and not be a header. 'sequence data' here is loosely defined as non-empty lines which do not start with '>' This will cause Color Space FASTA (csfasta) to be detected as True (they are, after all, still FASTA files - they have a header line followed by sequence data) Previously this method did some checking to determine if the sequence data had integers (presumably to differentiate between fasta and csfasta) This should be done through sniff order, where csfasta (currently has a null sniff function) is detected for first (stricter definition) followed sometime after by fasta We will only check that the first purported sequence is correctly formatted. 1 file(s) affected in this change: lib/galaxy/datatypes/sequence.py diffs (83 lines): diff -r 5c3736861e37 -r 64506c9397e4 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Thu Dec 11 15:09:37 2008 -0500 +++ b/lib/galaxy/datatypes/sequence.py Thu Dec 11 16:00:06 2008 -0500 @@ -34,7 +34,7 @@ dataset.peek = data.get_file_peek( dataset.file_name ) dataset.blurb = data.nice_size( dataset.get_size() ) - def sniff(self, filename): + def sniff( self, filename ): """ Determines whether the file is in fasta format @@ -42,7 +42,16 @@ The first character of the description line is a greater-than (">") symbol in the first column. All lines should be shorter than 80 charcters - For complete details see http://www.g2l.bio.uni-goettingen.de/blast/fastades.html + For complete details see http://www.ncbi.nlm.nih.gov/blast/fasta.shtml + + Rules for sniffing as True: + We don't care about line length (other than empty lines). + The first non-empty line must start with '>' and the Very Next line.strip() must have sequence data and not be a header. + 'sequence data' here is loosely defined as non-empty lines which do not start with '>' + This will cause Color Space FASTA (csfasta) to be detected as True (they are, after all, still FASTA files - they have a header line followed by sequence data) + Previously this method did some checking to determine if the sequence data had integers (presumably to differentiate between fasta and csfasta) + This should be done through sniff order, where csfasta (currently has a null sniff function) is detected for first (stricter definition) followed sometime after by fasta + We will only check that the first purported sequence is correctly formatted. >>> fname = get_test_fname( 'sequence.maf' ) >>> Fasta().sniff( fname ) @@ -51,34 +60,26 @@ >>> Fasta().sniff( fname ) True """ - headers = get_headers( filename, None ) - data_found = False + try: - if len(headers) > 1 and headers[0][0] and headers[0][0][0] == ">": - for i, l in enumerate( headers ): - line = l[0] - if i < 1: - continue - if line: - data_found = True - try: - int( line[0] ) - return False - except: - try: - elems = line.split() - int( elems[0] ) - return False - except: - return True - else: - return False - if data_found: - return True - else: - return False + fh = open( filename ) + while True: + line = fh.readline() + if not line: + break #EOF + line = line.strip() + if line: #first non-empty line + if line.startswith( '>' ): + #The next line.strip() must not be '', nor startwith '>' + line = fh.readline().strip() + if line == '' or line.startswith( '>' ): + break + return True + else: + break #we found a non-empty line, but its not a fasta header except: - return False + pass + return False class csFasta( Sequence ): """ Class representing the SOLID Color-Space sequence ( csfasta ) """

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[hg] galaxy 1659: New report showing last login for users, a few...
by Greg Von Kuster 12 Dec '08

12 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/cf461b1d6659 changeset: 1659:cf461b1d6659 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Dec 12 09:43:42 2008 -0500 description: New report showing last login for users, a few bug fixes and some code cleanup for the reports as well. 9 file(s) affected in this change: lib/galaxy/model/mapping.py lib/galaxy/webapps/reports/app.py lib/galaxy/webapps/reports/base/controller.py lib/galaxy/webapps/reports/controllers/system.py lib/galaxy/webapps/reports/controllers/users.py lib/galaxy/webapps/reports/templates/index.mako lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako lib/galaxy/webapps/reports/templates/users.mako lib/galaxy/webapps/reports/templates/users_last_access_date.mako diffs (352 lines): diff -r 64506c9397e4 -r cf461b1d6659 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Thu Dec 11 16:00:06 2008 -0500 +++ b/lib/galaxy/model/mapping.py Fri Dec 12 09:43:42 2008 -0500 @@ -299,6 +299,7 @@ assign_mapper( context, User, User.table, properties=dict( histories=relation( History, backref="user", order_by=desc(History.table.c.update_time) ), + galaxy_sessions=relation( GalaxySession, order_by=desc( GalaxySession.table.c.update_time ) ), stored_workflow_menu_entries=relation( StoredWorkflowMenuEntry, backref="user", cascade="all, delete-orphan", collection_class=ordering_list( 'order_index' ) ) diff -r 64506c9397e4 -r cf461b1d6659 lib/galaxy/webapps/reports/app.py --- a/lib/galaxy/webapps/reports/app.py Thu Dec 11 16:00:06 2008 -0500 +++ b/lib/galaxy/webapps/reports/app.py Fri Dec 12 09:43:42 2008 -0500 @@ -1,6 +1,5 @@ -import sys, os, atexit +import sys, config import galaxy.model -import config class UniverseApplication( object ): """Encapsulates the state of a Universe application""" diff -r 64506c9397e4 -r cf461b1d6659 lib/galaxy/webapps/reports/base/controller.py --- a/lib/galaxy/webapps/reports/base/controller.py Thu Dec 11 16:00:06 2008 -0500 +++ b/lib/galaxy/webapps/reports/base/controller.py Fri Dec 12 09:43:42 2008 -0500 @@ -2,7 +2,6 @@ import os, time, logging # Pieces of Galaxy to make global in every controller from galaxy import web, util -from Cheetah.Template import Template log = logging.getLogger( __name__ ) diff -r 64506c9397e4 -r cf461b1d6659 lib/galaxy/webapps/reports/controllers/system.py --- a/lib/galaxy/webapps/reports/controllers/system.py Thu Dec 11 16:00:06 2008 -0500 +++ b/lib/galaxy/webapps/reports/controllers/system.py Fri Dec 12 09:43:42 2008 -0500 @@ -37,7 +37,15 @@ deleted_histories_days, msg = self.deleted_histories( **kwd ) elif kwd['action'] == "deleted_datasets": deleted_datasets_days, msg = self.deleted_datasets( **kwd ) - return trans.fill_template( 'system.mako', file_path=file_path, disk_usage=disk_usage, datasets=datasets, file_size_str=file_size_str, userless_histories_days=userless_histories_days, deleted_histories_days=deleted_histories_days, deleted_datasets_days=deleted_datasets_days, msg=msg ) + return trans.fill_template( 'system.mako', + file_path=file_path, + disk_usage=disk_usage, + datasets=datasets, + file_size_str=file_size_str, + userless_histories_days=userless_histories_days, + deleted_histories_days=deleted_histories_days, + deleted_datasets_days=deleted_datasets_days, + msg=msg ) def userless_histories( self, **kwd ): """The number of userless histories and associated datasets that have not been updated for the specified number of days.""" diff -r 64506c9397e4 -r cf461b1d6659 lib/galaxy/webapps/reports/controllers/users.py --- a/lib/galaxy/webapps/reports/controllers/users.py Thu Dec 11 16:00:06 2008 -0500 +++ b/lib/galaxy/webapps/reports/controllers/users.py Fri Dec 12 09:43:42 2008 -0500 @@ -1,7 +1,9 @@ -from datetime import * +from datetime import datetime, timedelta +from time import strftime import calendar from galaxy.webapps.reports.base.controller import * import galaxy.model +from galaxy.model.orm import * import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) import sqlalchemy as sa @@ -10,23 +12,20 @@ class Users( BaseController ): @web.expose + def index( self, trans, **kwd ): + params = util.Params( kwd ) + msg = params.get( 'msg', '' ) + return trans.fill_template( 'users.mako', msg=msg ) + @web.expose def registered_users( self, trans, **kwd ): params = util.Params( kwd ) - msg = '' - engine = galaxy.model.mapping.metadata.engine - s = """ - SELECT - count(id) AS num_users - FROM - galaxy_user - """ - rows = engine.text( s ).execute().fetchall() - num_users = rows[0].num_users + msg = params.get( 'msg', '' ) + num_users = galaxy.model.User.query().count() return trans.fill_template( 'registered_users.mako', num_users=num_users, msg=msg ) @web.expose def registered_users_per_month( self, trans, **kwd ): params = util.Params( kwd ) - msg = '' + msg = params.get( 'msg', '' ) q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( galaxy.model.User.table.c.create_time ) ).label( 'date' ), sa.func.count( galaxy.model.User.table.c.id ).label( 'num_users' ) ), from_obj = [ galaxy.model.User.table ], @@ -42,7 +41,7 @@ @web.expose def specified_month( self, trans, **kwd ): params = util.Params( kwd ) - msg = '' + msg = params.get( 'msg', '' ) year, month = map( int, params.get( 'month', datetime.utcnow().strftime( "%Y-%m" ) ).split( "-" ) ) start_date = date( year, month, 1 ) end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] ) @@ -70,7 +69,7 @@ @web.expose def specified_date( self, trans, **kwd ): params = util.Params( kwd ) - msg = '' + msg = params.get( 'msg', '' ) year, month, day = map( int, params.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ).split( "-" ) ) start_date = date( year, month, day ) end_date = start_date + timedelta( days=1 ) @@ -95,3 +94,21 @@ day_of_month=day_of_month, users=users, msg=msg ) + @web.expose + def last_access_date( self, trans, **kwd ): + params = util.Params( kwd ) + msg = params.get( 'msg', '' ) + not_logged_in_for_days = params.get( 'not_logged_in_for_days', 0 ) + if not not_logged_in_for_days: + not_logged_in_for_days = 0 + cutoff_time = datetime.utcnow() - timedelta( days=int( not_logged_in_for_days ) ) + now = strftime( "%Y-%m-%d %H:%M:%S" ) + users = [] + for user in galaxy.model.User.query().order_by( galaxy.model.User.table.c.email ).all(): + last_galaxy_session = user.galaxy_sessions[ 0 ] + if last_galaxy_session.update_time < cutoff_time: + users.append( ( user.email, last_galaxy_session.update_time.strftime( "%Y-%m-%d" ) ) ) + return trans.fill_template( 'users_last_access_date.mako', + users=users, + not_logged_in_for_days=not_logged_in_for_days, + msg=msg ) diff -r 64506c9397e4 -r cf461b1d6659 lib/galaxy/webapps/reports/templates/index.mako --- a/lib/galaxy/webapps/reports/templates/index.mako Thu Dec 11 16:00:06 2008 -0500 +++ b/lib/galaxy/webapps/reports/templates/index.mako Fri Dec 12 09:43:42 2008 -0500 @@ -1,29 +1,88 @@ <%inherit file="/base_panels.mako"/> <%def name="main_body()"> - ## Display the available reports - <div class="body"> - <h3 align="center">Galaxy Reports</h3> - <table align="center" width="40%" class="colored"> - <tr><td><div class="reportTitle">Job Information</div></td></tr> - <tr><td><div class="reportBody"><a href="${h.url_for( controller='jobs', action='today_all' )}">Number of jobs today</a> - displays the total number of jobs for today</div></td></tr> - <tr><td><div class="reportBody"><a href="${h.url_for( controller='jobs', action='specified_month_all' )}">Number of jobs per day for current month</a> - displays days of the current month with the total number of jobs for each day</div></td></tr> - <tr><td><div class="reportBody"><a href="${h.url_for( controller='jobs', action='specified_month_in_error' )}">Number of jobs in error per day for current month</a> - displays days of the current month with the total number of jobs in error for each day</div></td></tr> - <tr><td><div class="reportBody"><a href="${h.url_for( controller='jobs', action='all_unfinished' )}">All unfinished jobs</a> - displays jobs that are currently in a "new" state, a "queued" state or a "running" state</div></td></tr> - <tr><td><div class="reportBody"><a href="${h.url_for( controller='jobs', action='per_month_all' )}">Number of jobs per month</a> - displays a list of months with the total number of jobs for each month</div></td></tr> - <tr><td><div class="reportBody"><a href="${h.url_for( controller='jobs', action='per_month_in_error' )}">Number of jobs in error per month</a> - displays a list of months with the total number of jobs in error for each month</div></td></tr> - <tr><td><div class="reportBody"><a href="${h.url_for( controller='jobs', action='per_user' )}">Number of jobs per user</a> - displays users sorted in descending order by the number of jobs they have submitted</div></td></tr> - <tr><td><div class="reportBody"><a href="${h.url_for( controller='jobs', action='per_tool' )}">Number of jobs per tool</a> - displays tools sorted in alphabetical order by tool id and the number of jobs created by the tool</div></td></tr> - <tr><td><div class="reportBody"><a href="${h.url_for( controller='jobs', action='per_domain' )}">Number of jobs per Internet domain</a> - displays the number of jobs that have been submitted per Internet domain</div></td></tr> - </table> - <br clear="left"/><br/><br/><br/> - <table align="center" width="40%" class="colored"> - <tr><td><div class="reportTitle">User Information</div></td></tr> - <tr><td><div class="reportBody"><a href="${h.url_for( controller='users', action='registered_users' )}">Number of registered users</a> - displays the total number of registered users</div></td></tr> - </table> - <br clear="left"/><br/><br/><br/> - <table align="center" width="40%" class="colored"> - <tr><td><div class="reportTitle">System Information</div></td></tr> - <tr><td><div class="reportBody"><a href="${h.url_for( controller='system', action='index' )}">Disk space, old histories and datasets</a> - displays history and dataset information including disk space allocation where datasets are stored</div></td></tr> - </table> - </div> + ## Display the available reports + <div class="body"> + <h3 align="center">Galaxy Reports</h3> + <table align="center" width="40%" class="colored"> + <tr><td><div class="reportTitle">Job Information</div></td></tr> + <tr> + <td> + <div class="reportBody"> + <a href="${h.url_for( controller='jobs', action='today_all' )}">Number of jobs today</a> - displays the total number of jobs for today + </div> + </td> + </tr> + <tr> + <td> + <div class="reportBody"> + <a href="${h.url_for( controller='jobs', action='specified_month_all' )}">Number of jobs per day for current month</a> - displays days of the current month with the total number of jobs for each day + </div> + </td> + </tr> + <tr> + <td> + <div class="reportBody"> + <a href="${h.url_for( controller='jobs', action='specified_month_in_error' )}">Number of jobs in error per day for current month</a> - displays days of the current month with the total number of jobs in error for each day + </div> + </td> + </tr> + <tr> + <td> + <div class="reportBody"> + <a href="${h.url_for( controller='jobs', action='all_unfinished' )}">All unfinished jobs</a> - displays jobs that are currently in a "new" state, a "queued" state or a "running" state + </div> + </td> + </tr> + <tr> + <td> + <div class="reportBody"> + <a href="${h.url_for( controller='jobs', action='per_month_all' )}">Number of jobs per month</a> - displays a list of months with the total number of jobs for each month + </div> + </td> + </tr> + <tr> + <td> + <div class="reportBody"> + <a href="${h.url_for( controller='jobs', action='per_month_in_error' )}">Number of jobs in error per month</a> - displays a list of months with the total number of jobs in error for each month + </div> + </td> + </tr> + <tr> + <td> + <div class="reportBody"> + <a href="${h.url_for( controller='jobs', action='per_user' )}">Number of jobs per user</a> - displays users sorted in descending order by the number of jobs they have submitted + </div> + </td> + </tr> + <tr> + <td> + <div class="reportBody"> + <a href="${h.url_for( controller='jobs', action='per_tool' )}">Number of jobs per tool</a> - displays tools sorted in alphabetical order by tool id and the number of jobs created by the tool + </div> + </td> + </tr> + </table> + <br clear="left"/><br/><br/><br/> + <table align="center" width="40%" class="colored"> + <tr><td><div class="reportTitle">User Information</div></td></tr> + <tr> + <td> + <div class="reportBody"> + <a href="${h.url_for( controller='users', action='index' )}">Users</a> - displays information about registered users + </div> + </td> + </tr> + </table> + <br clear="left"/><br/><br/><br/> + <table align="center" width="40%" class="colored"> + <tr><td><div class="reportTitle">System Information</div></td></tr> + <tr> + <td> + <div class="reportBody"> + <a href="${h.url_for( controller='system', action='index' )}">Disk space, old histories and datasets</a> - displays history and dataset information including disk space allocation where datasets are stored + </div> + </td> + </tr> + </table> + </div> </%def> diff -r 64506c9397e4 -r cf461b1d6659 lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako --- a/lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako Thu Dec 11 16:00:06 2008 -0500 +++ b/lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako Fri Dec 12 09:43:42 2008 -0500 @@ -2,7 +2,7 @@ <%def name="main_body()"> <div class="reportBody"> - <h3 align="center">All Jobs in Error for ${day_label}, ${month_label} ${day_of_month}, ${year_label} ( includes jobs deleted before finishing )</h3> + <h3 align="center">All Jobs in Error for ${day_label}, ${month_label} ${day_of_month}, ${year_label}</h3> %if msg: <table align="center" width="70%" class="border" cellpadding="5" cellspacing="5"> <tr><td class="ok_bgr">${msg}</td></tr> diff -r 64506c9397e4 -r cf461b1d6659 lib/galaxy/webapps/reports/templates/users.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/webapps/reports/templates/users.mako Fri Dec 12 09:43:42 2008 -0500 @@ -0,0 +1,29 @@ +<%inherit file="/base_panels.mako"/> + +<%def name="main_body()"> + <h3 align="center">Registered Users</h3> + %if msg: + <table align="center" width="70%" class="border" cellpadding="5" cellspacing="5"> + <tr><td class="ok_bgr">${msg}</td></tr> + </table> + %endif + <table align="center" width="40%" class="colored"> + <tr> + <td> + <div class="reportBody"> + <a href="${h.url_for( controller='users', action='registered_users' )}">Registered Users</a> - displays the number of registered users + </div> + </td> + </tr> + </table> + <br clear="left" /><br /> + <table align="center" width="40%" class="colored"> + <tr> + <td> + <div class="reportBody"> + <a href="${h.url_for( controller='users', action='last_access_date' )}">Date of Last Login</a> - displays users sorted by date of last login + </div> + </td> + </tr> + </table> +</%def> diff -r 64506c9397e4 -r cf461b1d6659 lib/galaxy/webapps/reports/templates/users_last_access_date.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/webapps/reports/templates/users_last_access_date.mako Fri Dec 12 09:43:42 2008 -0500 @@ -0,0 +1,46 @@ +<%inherit file="/base_panels.mako"/> + +<%def name="main_body()"> + <h3 align="center">Date of Last Galaxy Login</h3> + <h4 align="center">Listed in descending order by access date ( oldest date first )</h4> + %if msg: + <table align="center" width="70%" class="border" cellpadding="5" cellspacing="5"> + <tr><td class="ok_bgr">${msg}</td></tr> + </table> + %endif + <table align="center" width="70%" class="colored" cellpadding="5" cellspacing="5"> + <tr> + <td> + <form method="post" controller="users" action="last_access_date"> + <p> + Users that have not logged in to Galaxy for + <input type="textfield" value="${not_logged_in_for_days}" size="3" name="not_logged_in_for_days"> days. +  <button name="action" value="not_logged_in_for_days">Go</button> + </p> + </form> + </td> + </tr> + </table> + <table align="center" width="70%" class="colored" cellpadding="5" cellspacing="5"> + %if users: + <tr class="header"> + <td>Email</td> + <td>Date of last Login</td> + </tr> + <% ctr = 0 %> + %for user in users: + %if ctr % 2 == 1: + <tr class="odd_row"> + %else: + <tr class="tr"> + %endif + <td>${user[0]}</td> + <td>${user[1]}</td> + </tr> + <% ctr += 1 %> + %endfor + %else: + <tr><td>All users have logged in to Galaxy within the past ${not_logged_in_for_days} days</td></tr> + %endif + </table> +</%def>

1 0

[hg] galaxy 1657: Comment out logging for remote_user creation a...
by Nate Coraor 11 Dec '08

11 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/5c3736861e37 changeset: 1657:5c3736861e37 user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Dec 11 15:09:37 2008 -0500 description: Comment out logging for remote_user creation as a temporary fix 1 file(s) affected in this change: lib/galaxy/web/framework/__init__.py diffs (12 lines): diff -r 9a5bfe13e47b -r 5c3736861e37 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Thu Dec 11 12:18:00 2008 -0500 +++ b/lib/galaxy/web/framework/__init__.py Thu Dec 11 15:09:37 2008 -0500 @@ -274,7 +274,7 @@ user = self.app.model.User( email=remote_user_email ) user.set_password_cleartext( 'external' ) user.external = True - self.log_event( "Automatically created account '%s'", user.email ) + #self.log_event( "Automatically created account '%s'", user.email ) return user def __update_session_cookie( self ): """

1 0