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[hg] galaxy 1674: Enhancing incorrect_Gops_job script to output ...
by Nate Coraor 17 Dec '08

17 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/006bfb42e335 changeset: 1674:006bfb42e335 user: guru date: Wed Dec 17 11:01:57 2008 -0500 description: Enhancing incorrect_Gops_job script to output only those jobs whose output has changed since the BitSetSafeReaderWrapper was fixed. 1 file(s) affected in this change: scripts/others/incorrect_gops_jobs.py diffs (45 lines): diff -r f61f2128c692 -r 006bfb42e335 scripts/others/incorrect_gops_jobs.py --- a/scripts/others/incorrect_gops_jobs.py Tue Dec 16 17:30:19 2008 -0500 +++ b/scripts/others/incorrect_gops_jobs.py Wed Dec 17 11:01:57 2008 -0500 @@ -5,7 +5,7 @@ """ from galaxy import eggs -import sys, os, ConfigParser +import sys, os, ConfigParser, tempfile import galaxy.app import galaxy.model.mapping import pkg_resources @@ -62,6 +62,23 @@ history = app.model.History.get( hda.history_id ) print "# ------> processing history id %s" % str( history.id ) if history.user_id: + cmd_line = str( job.command_line ) + new_output = tempfile.NamedTemporaryFile('w') + if (sa.or_( app.model.Job.table.c.tool_id == 'gops_intersect_1', + app.model.Job.table.c.tool_id == 'gops_subtract_1', + app.model.Job.table.c.tool_id == 'gops_coverage_1' + ) + ): + new_cmd_line = " ".join(map(str,cmd_line.split()[:4])) + " " + new_output.name + " " + " ".join(map(str,cmd_line.split()[5:])) + job_output = cmd_line.split()[4] + else: + new_cmd_line = " ".join(map(str,cmd_line.split()[:3])) + " " + new_output.name + " " + " ".join(map(str,cmd_line.split()[4:])) + job_output = cmd_line.split()[3] + os.system(new_cmd_line) + diff_status = os.system('diff %s %s >> /dev/null' %(new_output.name, job_output)) + if diff_status == 0: + continue + print "# --------> Outputs differ" user = app.model.User.get( history.user_id ) jobs[ job.id ] = {} jobs[ job.id ][ 'hda_id' ] = hda.id @@ -77,7 +94,7 @@ print "\n\n# Number of incorrect Jobs: %d\n\n" % ( len( jobs ) ) print "#job_id\thda_id\thda_name\thda_info\thistory_id\thistory_name\thistory_update_time\tuser_email" for jid in jobs: - print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % \ + print '%s\t%s\t"%s"\t"%s"\t%s\t"%s"\t"%s"\t%s' % \ ( str( jid ), str( jobs[ jid ][ 'hda_id' ] ), jobs[ jid ][ 'hda_name' ],

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[hg] galaxy 1673: Allow workflows to recognize "data_meta" filte...
by Greg Von Kuster 17 Dec '08

17 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/f61f2128c692 changeset: 1673:f61f2128c692 user: James Taylor <james(a)jamestaylor.org> date: Tue Dec 16 17:30:19 2008 -0500 description: Allow workflows to recognize "data_meta" filters in dynamic options as forcing runtime validation. 2 file(s) affected in this change: lib/galaxy/tools/parameters/basic.py lib/galaxy/tools/parameters/dynamic_options.py diffs (59 lines): diff -r 79d9195e5899 -r f61f2128c692 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Tue Dec 16 14:31:00 2008 -0500 +++ b/lib/galaxy/tools/parameters/basic.py Tue Dec 16 17:30:19 2008 -0500 @@ -495,7 +495,7 @@ # Dynamic options are not yet supported in workflow, allow # specifying the value as text for now. if self.is_dynamic and trans.workflow_building_mode \ - and ( self.options is None or self.options.dataset_ref_name is not None ): + and ( self.options is None or self.options.has_dataset_dependencies ): assert isinstance( value, UnvalidatedValue ) value = value.value if self.multiple: @@ -519,7 +519,7 @@ # HACK: trans may be None here if doing late validation, this is # treated the same as not being in workflow mode if self.is_dynamic and ( trans and trans.workflow_building_mode ) \ - and ( self.options is None or self.options.dataset_ref_name is not None ): + and ( self.options is None or self.options.has_dataset_dependencies ): if self.multiple: value = value.split( "\n" ) return UnvalidatedValue( value ) @@ -560,7 +560,7 @@ def get_initial_value( self, trans, context ): # More working around dynamic options for workflow if self.is_dynamic and trans.workflow_building_mode \ - and ( self.options is None or self.options.dataset_ref_name is not None ): + and ( self.options is None or self.options.has_dataset_dependencies ): # Really the best we can do? return UnvalidatedValue( None ) options = list( self.get_options( trans, context ) ) diff -r 79d9195e5899 -r f61f2128c692 lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py Tue Dec 16 14:31:00 2008 -0500 +++ b/lib/galaxy/tools/parameters/dynamic_options.py Tue Dec 16 17:30:19 2008 -0500 @@ -78,6 +78,7 @@ Filter.__init__( self, d_option, elem ) self.ref_name = elem.get( "ref", None ) assert self.ref_name is not None, "Required 'ref' attribute missing from filter" + d_option.has_dataset_dependencies = True self.key = elem.get( "key", None ) assert self.key is not None, "Required 'key' attribute missing from filter" self.column = elem.get( "column", None ) @@ -290,6 +291,9 @@ self.file_fields = None self.largest_index = 0 self.dataset_ref_name = None + # True if the options generation depends on one or more other parameters + # that are dataset inputs + self.has_dataset_dependencies = False self.validators = [] self.converter_safe = True @@ -320,6 +324,7 @@ self.file_fields = self.parse_file_fields( open( data_file ) ) elif dataset_file is not None: self.dataset_ref_name = dataset_file + self.has_dataset_dependencies = True self.converter_safe = False elif from_parameter is not None: transform_lines = elem.get( 'transform_lines', None )

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[hg] galaxy 1672: Update bx-python to r459
by Nate Coraor 16 Dec '08

16 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/79d9195e5899 changeset: 1672:79d9195e5899 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Dec 16 14:31:00 2008 -0500 description: Update bx-python to r459 1 file(s) affected in this change: eggs.ini diffs (18 lines): diff -r 87f793e3dce5 -r 79d9195e5899 eggs.ini --- a/eggs.ini Tue Dec 16 10:04:30 2008 -0500 +++ b/eggs.ini Tue Dec 16 14:31:00 2008 -0500 @@ -55,12 +55,12 @@ MySQL_python = _5.0.67_static python_lzo = _static flup = .dev_r2311 -bx_python = _dev_r458 +bx_python = _dev_r459 nose = .dev_r101 ; source location, necessary for scrambling [source] -bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r458.tar.bz2 +bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r459.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 1671: Server errors thrown when switching between Ga...
by Greg Von Kuster 16 Dec '08

16 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/87f793e3dce5 changeset: 1671:87f793e3dce5 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Dec 16 10:04:30 2008 -0500 description: Server errors thrown when switching between Galaxy and reports in the same browser was due to the id_secret being different in the Galaxy config and the reports config, so add comments to ensure this is not repeated. 4 file(s) affected in this change: lib/galaxy/config.py lib/galaxy/webapps/reports/config.py reports_wsgi.ini.sample universe_wsgi.ini.sample diffs (79 lines): diff -r cdb2935dc336 -r 87f793e3dce5 lib/galaxy/config.py --- a/lib/galaxy/config.py Mon Dec 15 17:04:06 2008 -0500 +++ b/lib/galaxy/config.py Tue Dec 16 10:04:30 2008 -0500 @@ -35,6 +35,9 @@ self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) self.tool_config = resolve_path( kwargs.get( 'tool_config_file', 'tool_conf.xml' ), self.root ) self.tool_secret = kwargs.get( "tool_secret", "" ) + # CRITICAL: the value of id_secret MUST be the same in universe_wsgi.ini and reports_wsgi.ini + # or the framework's __ensure_valid_session method will throw exceptions when switching between + # Galaxy and the reports in the same browser. self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) ) self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None ) diff -r cdb2935dc336 -r 87f793e3dce5 lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py Mon Dec 15 17:04:06 2008 -0500 +++ b/lib/galaxy/webapps/reports/config.py Tue Dec 16 10:04:30 2008 -0500 @@ -25,14 +25,14 @@ # Where dataset files are stored self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root ) self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root ) + # CRITICAL: the value of id_secret MUST be the same in universe_wsgi.ini and reports_wsgi.ini + # or the framework's __ensure_valid_session method will throw exceptions when switching between + # Galaxy and the reports in the same browser. self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) ) self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/reports/compiled_templates" ), self.root ) - self.admin_pass = kwargs.get('admin_pass',"galaxy") self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail") - self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join(a)bx.psu.edu") - self.error_email_to = kwargs.get( 'error_email_to', None ) self.brand = kwargs.get( 'brand', None ) self.wiki_url = kwargs.get( 'wiki_url', "http://g2.trac.bx.psu.edu/" ) self.bugs_email = kwargs.get( 'bugs_email', "mailto:galaxy-bugs@bx.psu.edu" ) diff -r cdb2935dc336 -r 87f793e3dce5 reports_wsgi.ini.sample --- a/reports_wsgi.ini.sample Mon Dec 15 17:04:06 2008 -0500 +++ b/reports_wsgi.ini.sample Tue Dec 16 10:04:30 2008 -0500 @@ -36,15 +36,16 @@ session_key = galaxysessions session_secret = changethisinproduction +# Galaxy session security +# The value of id_secret MUST be the same as the value of id_secret in universe_wsgi.ini +id_secret = changethisinproductiontoo + # Configuration for debugging middleware debug = true use_lint = false # NEVER enable this on a public site (even test or QA) # use_interactive = true - -# Admin Password -admin_pass = "galaxy" # path to sendmail sendmail_path = /usr/sbin/sendmail @@ -58,10 +59,6 @@ # Profiling middleware (cProfile based) ## use_profile = True -# Mail -smtp_server = coltrane.bx.psu.edu -error_email_to = galaxy_bugs(a)bx.psu.edu - # Use the new iframe / javascript based layout use_new_layout = true diff -r cdb2935dc336 -r 87f793e3dce5 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Mon Dec 15 17:04:06 2008 -0500 +++ b/universe_wsgi.ini.sample Tue Dec 16 10:04:30 2008 -0500 @@ -73,6 +73,7 @@ session_secret = changethisinproduction # Galaxy session security +# The value of id_secret MUST be the same as the value of id_secret in reports_wsgi.ini id_secret = changethisinproductiontoo # Use user provided in an upstream server's $REMOTE_USER variable

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[hg] galaxy 1666: Attempting to merge conflicts.
by Greg Von Kuster 15 Dec '08

15 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/ced77aa5f967 changeset: 1666:ced77aa5f967 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Dec 15 08:58:33 2008 -0500 description: Attempting to merge conflicts. 1 file(s) affected in this change: tools/data_source/gbrowse_datasource.py diffs (55 lines): diff -r 503fcdb79851 -r ced77aa5f967 tools/data_source/gbrowse_datasource.py --- a/tools/data_source/gbrowse_datasource.py Mon Dec 15 08:55:16 2008 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,51 +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 - -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__()

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[hg] galaxy 1669: Fix for the users reports.
by Greg Von Kuster 15 Dec '08

15 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/493a4a3ec2d8 changeset: 1669:493a4a3ec2d8 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Dec 15 11:25:47 2008 -0500 description: Fix for the users reports. 1 file(s) affected in this change: lib/galaxy/webapps/reports/controllers/users.py diffs (18 lines): diff -r 87a9cf297998 -r 493a4a3ec2d8 lib/galaxy/webapps/reports/controllers/users.py --- a/lib/galaxy/webapps/reports/controllers/users.py Mon Dec 15 10:37:39 2008 -0500 +++ b/lib/galaxy/webapps/reports/controllers/users.py Mon Dec 15 11:25:47 2008 -0500 @@ -1,4 +1,4 @@ -from datetime import datetime, timedelta +from datetime import * from time import strftime import calendar, operator from galaxy.webapps.reports.base.controller import * @@ -98,7 +98,7 @@ 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 ) + not_logged_in_for_days = params.get( 'not_logged_in_for_days', 90 ) if not not_logged_in_for_days: not_logged_in_for_days = 0 cutoff_time = datetime.utcnow() - timedelta( days=int( not_logged_in_for_days ) )

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[hg] galaxy 1667: Reset functional test port which somehow got c...
by Greg Von Kuster 15 Dec '08

15 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/3a0b07161c1a changeset: 1667:3a0b07161c1a user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Dec 15 09:06:11 2008 -0500 description: Reset functional test port which somehow got committed when attempting to merge conflicts. 1 file(s) affected in this change: test/functional/__init__.py diffs (12 lines): diff -r ced77aa5f967 -r 3a0b07161c1a test/functional/__init__.py --- a/test/functional/__init__.py Mon Dec 15 08:58:33 2008 -0500 +++ b/test/functional/__init__.py Mon Dec 15 09:06:11 2008 -0500 @@ -24,7 +24,7 @@ # server (for running the tests against a running instance) default_galaxy_test_host = "localhost" -default_galaxy_test_port = "9879" +default_galaxy_test_port = "9999" galaxy_test_file_dir = "test-data" server = None app = None

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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 1665: merging heads
by Greg Von Kuster 15 Dec '08

15 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/503fcdb79851 changeset: 1665:503fcdb79851 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Dec 15 08:55:16 2008 -0500 description: merging heads 3 file(s) affected in this change: lib/galaxy/web/framework/__init__.py test/functional/__init__.py tools/data_source/gbrowse_datasource.py diffs (116 lines): diff -r 5f4511a5b4d6 -r 503fcdb79851 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Sat Dec 13 23:35:29 2008 -0500 +++ b/lib/galaxy/web/framework/__init__.py Mon Dec 15 08:55:16 2008 -0500 @@ -105,6 +105,8 @@ self.app = app self.webapp = webapp self.security = webapp.security + # FIXME: the following 3 attributes are not currently used + # Remove them if they are not going to be... self.__user = NOT_SET self.__history = NOT_SET self.__galaxy_session = NOT_SET @@ -178,9 +180,17 @@ Support for universe_session and universe_user cookies has been removed as of 31 Oct 2008. """ + #log.debug("####In __ensure_valid_session...") + #try: + # log.debug("####In __ensure_valid_session, self.galaxy_session: %s" % str( self.galaxy_session ) ) + # log.debug("####In __ensure_valid_session, self.galaxy_session.is_valid: %s" % str(self.galaxy_session.is_valid)) + #except: + # log.debug("####In __ensure_valid_session, self.galaxy_session does not yet exist...") sa_session = self.sa_session # Try to load an existing session + #log.debug("###In __ensure_valid_session, before secure_id = self.get_cookie( name='galaxysession' )...") secure_id = self.get_cookie( name='galaxysession' ) + #log.debug("###In __ensure_valid_session, secure_id: %s" % str( secure_id) ) galaxy_session = None prev_galaxy_session = None user_for_new_session = None @@ -191,8 +201,10 @@ if secure_id: # Decode the cookie value to get the session_key session_key = self.security.decode_session_key( secure_id ) + #log.debug("###In __ensure_valid_session, session_key: %s" % str( session_key) ) # Retrive the galaxy_session id via the unique session_key galaxy_session = sa_session.query( self.app.model.GalaxySession ).filter_by( session_key=session_key, is_valid=True ).first() + #log.debug("###In __ensure_valid_session, galaxy_session: %s" % str( galaxy_session) ) # If remote user is in use it can invalidate the session, so we need to # to check some things now. if self.app.config.use_remote_user: @@ -248,6 +260,7 @@ Caller is responsible for flushing the returned session. """ + #log.debug("###In __create_new_session...") session_key = self.security.get_new_session_key() galaxy_session = self.app.model.GalaxySession( session_key=session_key, diff -r 5f4511a5b4d6 -r 503fcdb79851 test/functional/__init__.py --- a/test/functional/__init__.py Sat Dec 13 23:35:29 2008 -0500 +++ b/test/functional/__init__.py Mon Dec 15 08:55:16 2008 -0500 @@ -24,7 +24,7 @@ # server (for running the tests against a running instance) default_galaxy_test_host = "localhost" -default_galaxy_test_port = "9999" +default_galaxy_test_port = "9879" galaxy_test_file_dir = "test-data" server = None app = None diff -r 5f4511a5b4d6 -r 503fcdb79851 tools/data_source/gbrowse_datasource.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/gbrowse_datasource.py Mon Dec 15 08:55:16 2008 -0500 @@ -0,0 +1,51 @@ +#!/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 + +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__()

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[hg] galaxy 1670: Some code cleanup in framework/__init__.py
by Greg Von Kuster 15 Dec '08

15 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/cdb2935dc336 changeset: 1670:cdb2935dc336 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Dec 15 17:04:06 2008 -0500 description: Some code cleanup in framework/__init__.py 1 file(s) affected in this change: lib/galaxy/web/framework/__init__.py diffs (62 lines): diff -r 493a4a3ec2d8 -r cdb2935dc336 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Mon Dec 15 11:25:47 2008 -0500 +++ b/lib/galaxy/web/framework/__init__.py Mon Dec 15 17:04:06 2008 -0500 @@ -25,7 +25,7 @@ import mako.lookup pkg_resources.require( "SQLAlchemy >= 0.4" ) -from sqlalchemy import desc +from sqlalchemy import and_ import logging log = logging.getLogger( __name__ ) @@ -180,17 +180,9 @@ Support for universe_session and universe_user cookies has been removed as of 31 Oct 2008. """ - #log.debug("####In __ensure_valid_session...") - #try: - # log.debug("####In __ensure_valid_session, self.galaxy_session: %s" % str( self.galaxy_session ) ) - # log.debug("####In __ensure_valid_session, self.galaxy_session.is_valid: %s" % str(self.galaxy_session.is_valid)) - #except: - # log.debug("####In __ensure_valid_session, self.galaxy_session does not yet exist...") sa_session = self.sa_session # Try to load an existing session - #log.debug("###In __ensure_valid_session, before secure_id = self.get_cookie( name='galaxysession' )...") secure_id = self.get_cookie( name='galaxysession' ) - #log.debug("###In __ensure_valid_session, secure_id: %s" % str( secure_id) ) galaxy_session = None prev_galaxy_session = None user_for_new_session = None @@ -201,10 +193,9 @@ if secure_id: # Decode the cookie value to get the session_key session_key = self.security.decode_session_key( secure_id ) - #log.debug("###In __ensure_valid_session, session_key: %s" % str( session_key) ) - # Retrive the galaxy_session id via the unique session_key - galaxy_session = sa_session.query( self.app.model.GalaxySession ).filter_by( session_key=session_key, is_valid=True ).first() - #log.debug("###In __ensure_valid_session, galaxy_session: %s" % str( galaxy_session) ) + # Retrieve the galaxy_session id via the unique session_key + galaxy_session = self.app.model.GalaxySession.filter( and_( self.app.model.GalaxySession.table.c.session_key==session_key, + self.app.model.GalaxySession.table.c.is_valid==True ) ).first() # If remote user is in use it can invalidate the session, so we need to # to check some things now. if self.app.config.use_remote_user: @@ -260,7 +251,6 @@ Caller is responsible for flushing the returned session. """ - #log.debug("###In __create_new_session...") session_key = self.security.get_new_session_key() galaxy_session = self.app.model.GalaxySession( session_key=session_key, @@ -293,8 +283,7 @@ """ Update the 'galaxysession' cookie to match the current session. """ - self.set_cookie( name='galaxysession', - value=self.security.encode_session_key( self.galaxy_session.session_key ) ) + self.set_cookie( self.security.encode_session_key( self.galaxy_session.session_key ), name='galaxysession' ) def handle_user_login( self, user ): """

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