galaxy-dev May 2009

galaxy-dev@lists.galaxyproject.org

9 participants
41 discussions

How to make Galaxy link to a local installed UCSC database?
by xue dong 11 Jun '09

11 Jun '09

Hallo every one, I am new to Galaxy, I have a idea which maybe not new to people here. I work on arabidopsis. maybe you know that UCSC do not offer the genome assembly for plant. so i will install UCSC locally and built the genome assembly for arabidopsis. this work is half done now. I also installed Galaxy, if i understand correctly, Galaxy has the link to UCSC so the user can get data from UCSC. since what i interested is arabidopsis information, I hope Galaxy can retrive data form the locally installed UCSC in future. I do not know if it is possible to make this idea come ture.maybe some of you have done it. if yes, I am gratefully if you can tell me the how to get it. many thanks, Xue

2 1

Round-Robin Scheduling
by Assaf Gordon 10 Jun '09

10 Jun '09

Hello, I have another question regarding the local job scheduler: Is it possible to limit the number of jobs *per user* ? That is - any given user can have up to X number of jobs running concurrently, regardless of the value of local_job_queue_workers ? Imagine the following situation: local_job_queue_worker = 5 job_scheduler_policy = galaxy.jobs.schedulingpolicy.roundrobin:UserRoundRobin Which means that at any given moment, galaxy can run only five jobs. Now, Galaxy is completely Idle, no jobs are running. One users starts 7 very long running jobs (each jobs will take about two hours). If I understand correctly - since no jobs are running, 5 of the user's job will be started immediately, even with the round-robin policy, right ? And this means that for the next two hours, every other user which starts a job - his/her job will be either new or limbo-running, but none will actually be started, right ? I think I'm experiencing this situation on my galaxy server. Users are complaining their jobs have been running 'forever' or not even starting for a long long time. Close examination shows that there are running 5 jobs (all from the same user) which have been running for three hours, and they are kind of hogging all the worker threads. To make a long story short - I would like to make sure a single user can't hog Galaxy. Is it possible with the local job runner, and if not - is it possible with the SGE job runner ? Thanks for reading so far, Gordon.

2 1

Wrappers for Sequence Alignment Programs
by SHAUN WEBB 10 Jun '09

10 Jun '09

Hi, I am planning on integrating sequence alignment programs to our local instance of Galaxy. I was wondering if anyone else has developed wrappers for the following programs: Maq, Bowtie, Tophat. Also, is there a central repository for any new tools or wrappers that have been created by other developers? It would certainly be a useful resource and if I need to wrap these tools myself I would be happy share the code. Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

2 1

[hg] galaxy 2421: Add a defaulttimeout setting of 10 minutes to ...
by Greg Von Kuster 29 May '09

29 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/186fcb977e75 changeset: 2421:186fcb977e75 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu May 28 11:10:44 2009 -0400 description: Add a defaulttimeout setting of 10 minutes to the urlopen() call for requests to remote data sources. 1 file(s) affected in this change: tools/data_source/data_source.py diffs (43 lines): diff -r 5c2d30d3fb04 -r 186fcb977e75 tools/data_source/data_source.py --- a/tools/data_source/data_source.py Wed May 27 14:19:59 2009 -0400 +++ b/tools/data_source/data_source.py Thu May 28 11:10:44 2009 -0400 @@ -1,8 +1,8 @@ #!/usr/bin/env python -#Retreives data from UCSC and stores in a file. UCSC parameters are provided in the input/output file. -import urllib, sys, os, gzip, tempfile, shutil +# Retrieves data from external data source applications and stores in a dataset file. +# Data source application parameters are temporarily stored in the dataset file. +import socket, urllib, sys, os, gzip, tempfile, shutil from galaxy import eggs -#from galaxy.datatypes import data from galaxy.util import gzip_magic assert sys.version_info[:2] >= ( 2, 4 ) @@ -34,15 +34,23 @@ open( filename, 'w' ).write( "" ) stop_err( 'The remote data source application has not sent back a URL parameter in the request.' ) URL_method = params.get( 'URL_method', None ) - out = open( filename, 'w' ) - CHUNK_SIZE = 2**20 # 1Mb + CHUNK_SIZE = 2**20 # 1Mb + # The Python support for fetching resources from the web is layered. urllib uses the httplib + # library, which in turn uses the socket library. As of Python 2.3 you can specify how long + # a socket should wait for a response before timing out. By default the socket module has no + # timeout and can hang. Currently, the socket timeout is not exposed at the httplib or urllib2 + # levels. However, you can set the default timeout ( in seconds ) globally for all sockets by + # doing the following. + socket.setdefaulttimeout( 600 ) + # The following calls to urllib2.urlopen() will use the above default timeout try: if not URL_method or URL_method == 'get': page = urllib.urlopen( URL ) elif URL_method == 'post': page = urllib.urlopen( URL, urllib.urlencode( params ) ) - except: - stop_err( 'It appears that the remote data source application is currently off line. Please try again later.' ) + except Exception, e: + stop_err( 'The remote data source application may be off line, please try again later. Error: %s' % str( e ) ) + out = open( filename, 'w' ) while 1: chunk = page.read( CHUNK_SIZE ) if not chunk:

1 0

[hg] galaxy 2422: Fix for DrillDownParameter when no option is s...
by Greg Von Kuster 29 May '09

29 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/a07e84e73b45 changeset: 2422:a07e84e73b45 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu May 28 13:58:56 2009 -0400 description: Fix for DrillDownParameter when no option is selected and saved in worflow editing. 1 file(s) affected in this change: lib/galaxy/tools/parameters/basic.py diffs (15 lines): diff -r 186fcb977e75 -r a07e84e73b45 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Thu May 28 11:10:44 2009 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Thu May 28 13:58:56 2009 -0400 @@ -947,7 +947,10 @@ def from_html( self, value, trans=None, other_values={} ): if self.need_late_validation( trans, other_values ): if self.multiple: - value = value.split( "\n" ) + if value == '': #No option selected + value = None + else: + value = value.split( "\n" ) return UnvalidatedValue( value ) if not value: return None if not isinstance( value, list ):

1 0

[hg] galaxy 2423: Fix the cleanup_datasets script
by Greg Von Kuster 29 May '09

29 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/7a6f75bf4be5 changeset: 2423:7a6f75bf4be5 user: Nate Coraor <nate(a)bx.psu.edu> date: Thu May 28 15:18:49 2009 -0400 description: Fix the cleanup_datasets script 1 file(s) affected in this change: scripts/cleanup_datasets/cleanup_datasets.py diffs (17 lines): diff -r a07e84e73b45 -r 7a6f75bf4be5 scripts/cleanup_datasets/cleanup_datasets.py --- a/scripts/cleanup_datasets/cleanup_datasets.py Thu May 28 13:58:56 2009 -0400 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Thu May 28 15:18:49 2009 -0400 @@ -264,8 +264,13 @@ if dataset.extra_files_path and os.path.exists( dataset.extra_files_path ): shutil.rmtree( dataset.extra_files_path ) #we need to delete the directory and its contents; os.unlink would always fail on a directory dataset.purged = True + dataset.flush() else: print "# This dataset (%i) is not purgable, the file (%s) will not be removed.\n" % ( dataset.id, dataset.file_name ) + except OSError, exc: + print "# Error, file has already been removed: %s" % str( exc ) + dataset.purged = True + dataset.flush() except Exception, exc: print "# Error, exception: %s caught attempting to purge %s\n" %( str( exc ), dataset.file_name ) else:

1 0

[hg] galaxy 2420: Add tool config for GrameneMart data source.
by Greg Von Kuster 27 May '09

27 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5c2d30d3fb04 changeset: 2420:5c2d30d3fb04 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed May 27 14:19:59 2009 -0400 description: Add tool config for GrameneMart data source. 3 file(s) affected in this change: tool_conf.xml.main tool_conf.xml.sample tools/data_source/gramene_mart.xml diffs (67 lines): diff -r 1acbcbcebeb3 -r 5c2d30d3fb04 tool_conf.xml.main --- a/tool_conf.xml.main Wed May 27 11:15:35 2009 -0400 +++ b/tool_conf.xml.main Wed May 27 14:19:59 2009 -0400 @@ -6,6 +6,7 @@ <tool file="data_source/ucsc_tablebrowser_archaea.xml" /> <tool file="data_source/microbial_import.xml" /> <tool file="data_source/biomart.xml" /> + <tool file="data_source/gramene_mart.xml" /> <tool file="data_source/flymine.xml" /> <tool file="data_source/encode_db.xml" /> <tool file="data_source/epigraph_import.xml" /> diff -r 1acbcbcebeb3 -r 5c2d30d3fb04 tool_conf.xml.sample --- a/tool_conf.xml.sample Wed May 27 11:15:35 2009 -0400 +++ b/tool_conf.xml.sample Wed May 27 14:19:59 2009 -0400 @@ -8,6 +8,7 @@ <tool file="data_source/microbial_import.xml" /> <tool file="data_source/biomart.xml" /> <tool file="data_source/biomart_test.xml" /> + <tool file="data_source/gramene_mart.xml" /> <tool file="data_source/wormbase.xml" /> <tool file="data_source/wormbase_test.xml" /> <tool file="data_source/flymine.xml" /> diff -r 1acbcbcebeb3 -r 5c2d30d3fb04 tools/data_source/gramene_mart.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/gramene_mart.xml Wed May 27 14:19:59 2009 -0400 @@ -0,0 +1,41 @@ +<?xml version="1.0"?> + +<tool name="GrameneMart" id="gramenemart" tool_type="data_source" URL_method="get" version="1.0.1"> + <description> Central server</description> + <command interpreter="python">data_source.py $output</command> + <inputs action="http://www.gramene.org/biomart/martview" check_values="false" method="get" target="_top"> + <display>go to GrameneMart Central $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" /> + </inputs> + <request_param_translation> + <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="data_type" remote_name="exportView_outputformat" missing="tabular"> + <data_type_translation> + <format galaxy_format="tabular" remote_format="TSV" /> + </data_type_translation> + </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="" /> + <request_param galaxy_name="description" remote_name="description" missing="" /> + <request_param galaxy_name="name" remote_name="name" missing="Biomart query" /> + <request_param galaxy_name="info" remote_name="info" missing="" /> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="tabular" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool>

1 0

[hg] galaxy 2419: Add a hack to force UCSC links to be rewritten...
by Greg Von Kuster 27 May '09

27 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/1acbcbcebeb3 changeset: 2419:1acbcbcebeb3 user: Nate Coraor <nate(a)bx.psu.edu> date: Wed May 27 11:15:35 2009 -0400 description: Add a hack to force UCSC links to be rewritten as http if your upstream uses https 1 file(s) affected in this change: lib/galaxy/datatypes/interval.py diffs (16 lines): diff -r 7414f90d7eae -r 1acbcbcebeb3 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Tue May 26 16:35:23 2009 -0400 +++ b/lib/galaxy/datatypes/interval.py Wed May 27 11:15:35 2009 -0400 @@ -223,6 +223,12 @@ stop = viewport_tuple[2] for site_name, site_url in util.get_ucsc_by_build(dataset.dbkey): if site_name in app.config.ucsc_display_sites: + # HACK: UCSC doesn't support https, so force http even + # if our URL scheme is https. Making this work + # requires additional hackery in your upstream proxy. + # If UCSC ever supports https, remove this hack. + if base_url.startswith( 'https://' ): + base_url = base_url.replace( 'https', 'http', 1 ) display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s" % (base_url, url_for( controller='root' ), dataset.id, type) ) link = "%sdb=%s&position=%s:%s-%s&hgt.customText=%s" % (site_url, dataset.dbkey, chrom, start, stop, display_url ) ret_val.append( (site_name, link) )

1 0

[hg] galaxy 2418: Bug fix for undeleting deleted history items.
by Greg Von Kuster 27 May '09

27 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/7414f90d7eae changeset: 2418:7414f90d7eae user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue May 26 16:35:23 2009 -0400 description: Bug fix for undeleting deleted history items. 1 file(s) affected in this change: lib/galaxy/web/controllers/dataset.py diffs (52 lines): diff -r 76890d7fb3dd -r 7414f90d7eae lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Tue May 26 14:59:40 2009 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Tue May 26 16:35:23 2009 -0400 @@ -127,27 +127,31 @@ return trans.show_error_message( "You are not allowed to access this dataset" ) def _undelete( self, trans, id ): - if isinstance( id, type( 1 ) ): - history = trans.get_history() - data = self.app.model.HistoryDatasetAssociation.get( id ) - if data and data.undeletable: - # Walk up parent datasets to find the containing history - topmost_parent = data - while topmost_parent.parent: - topmost_parent = topmost_parent.parent - assert topmost_parent in history.datasets, "Data does not belong to current history" - # Mark undeleted - data.mark_undeleted() - self.app.model.flush() - trans.log_event( "Dataset id %s has been undeleted" % str(id) ) - return True + try: + id = int( id ) + except ValueError, e: + return False + history = trans.get_history() + data = self.app.model.HistoryDatasetAssociation.get( id ) + if data and data.undeletable: + # Walk up parent datasets to find the containing history + topmost_parent = data + while topmost_parent.parent: + topmost_parent = topmost_parent.parent + assert topmost_parent in history.datasets, "Data does not belong to current history" + # Mark undeleted + data.mark_undeleted() + self.app.model.flush() + trans.log_event( "Dataset id %s has been undeleted" % str(id) ) + return True return False @web.expose def undelete( self, trans, id ): - self._undelete( trans, id ) - return trans.response.send_redirect( web.url_for( controller='root', action='history', show_deleted = True ) ) - + if self._undelete( trans, id ): + return trans.response.send_redirect( web.url_for( controller='root', action='history', show_deleted = True ) ) + raise "Error undeleting" + @web.expose def undelete_async( self, trans, id ): if self._undelete( trans, id ):

1 0

[hg] galaxy 2416: Bug fixes for the new security and libraries f...
by Greg Von Kuster 26 May '09

26 May '09

details: http://www.bx.psu.edu/hg/galaxy/rev/48e4b965545b changeset: 2416:48e4b965545b user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue May 26 14:32:18 2009 -0400 description: Bug fixes for the new security and libraries functional tests. 3 file(s) affected in this change: lib/galaxy/web/controllers/admin.py test/base/twilltestcase.py test/functional/test_security_and_libraries.py diffs (253 lines): diff -r 386e245f8076 -r 48e4b965545b lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Thu May 21 15:48:39 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Tue May 26 14:32:18 2009 -0400 @@ -875,14 +875,21 @@ library_folder.deleted = True library_folder.purged = True library_folder.flush() - purge_folder( library.root_folder ) - library.purged = True - library.flush() - msg = "Library '%s' and all of its contents have been purged, datasets will be removed from disk via the cleanup_datasets script" % library.name - return trans.response.send_redirect( web.url_for( controller='admin', - action='deleted_libraries', - msg=util.sanitize_text( msg ), - messagetype='done' ) ) + if not library.deleted: + msg = "Library '%s' has not been marked deleted, so it cannot be purged" % ( library.name ) + return trans.response.send_redirect( web.url_for( controller='admin', + action='browse_libraries', + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + else: + purge_folder( library.root_folder ) + library.purged = True + library.flush() + msg = "Library '%s' and all of its contents have been purged, datasets will be removed from disk via the cleanup_datasets script" % library.name + return trans.response.send_redirect( web.url_for( controller='admin', + action='deleted_libraries', + msg=util.sanitize_text( msg ), + messagetype='done' ) ) @web.expose @web.require_admin def folder( self, trans, id, library_id, **kwd ): @@ -1545,7 +1552,7 @@ messagetype=messagetype ) @web.expose @web.require_admin - def info_template( self, trans, library_id, id=None, num_fields=0, folder_id=None, ldda_id=None, library_dataset_id=None, **kwd ): + def info_template( self, trans, library_id, id=None, num_fields=0, folder_id=None, ldda_id=None, library_dataset_id=None, **kwd ): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) diff -r 386e245f8076 -r 48e4b965545b test/base/twilltestcase.py --- a/test/base/twilltestcase.py Thu May 21 15:48:39 2009 -0400 +++ b/test/base/twilltestcase.py Tue May 26 14:32:18 2009 -0400 @@ -855,9 +855,14 @@ tc.fv( '1', 'new_element_name_0', ele_name_0 ) tc.fv( '1', 'new_element_name_1', ele_name_1 ) tc.submit( 'new_info_template_button' ) + self.check_page_for_string( 'The new information template has been created.' ) self.home() - def add_library_info_template_element( self, library_id, template_id, template_name, ele_name_1, ele_desc_1, - ele_name_2, ele_desc_2, new_ele_name='Fubar', new_ele_desc='This is the Fubar compnent' ): + def add_library_info_template_element( self, library_id, template_id, template_name, + ele_field_name_1, ele_name_1, + ele_field_desc_1, ele_desc_1, + ele_field_name_2, ele_name_2, + ele_field_desc_2, ele_desc_2, + new_ele_name='Fubar', new_ele_desc='This is the Fubar compnent' ): """Add a new element to an existing library info template""" self.home() url = "%s/admin/info_template?library_id=%s&id=%s&edit_template=True&num_fields=1&edit_info_template_button=Save" % \ @@ -868,10 +873,10 @@ tc.fv( '1', 'id', template_id ) tc.fv( '1', 'set_num_fields', '0' ) tc.fv( '1', 'name', template_name ) - tc.fv( '1', 'element_name_1', ele_name_1 ) - tc.fv( '1', 'element_description_1', ele_desc_1 ) - tc.fv( '1', 'element_name_2', ele_name_2 ) - tc.fv( '1', 'element_description_2', ele_desc_2 ) + tc.fv( '1', ele_field_name_1, ele_name_1 ) + tc.fv( '1', ele_field_desc_1, ele_desc_1 ) + tc.fv( '1', ele_field_name_2, ele_name_2 ) + tc.fv( '1', ele_field_desc_2, ele_desc_2 ) tc.fv( '1', 'new_element_name_0', new_ele_name ) tc.fv( '1', 'new_element_description_0', new_ele_desc ) tc.submit( 'edit_info_template_button' ) @@ -888,7 +893,8 @@ tc.fv( '2', ele_2_field_name, ele_2_contents ) tc.submit( 'create_new_info_button' ) self.home() - def edit_library_info_template( self, library_id, id, name, name_1, desc_1, name_2, desc_2 ): + def edit_library_info_template( self, library_id, id, name, ele_name_1, name_1, + ele_desc_1, desc_1, ele_name_2, name_2, ele_desc_2, desc_2 ): """Edit an existing library info template""" self.home() url = "%s/admin/info_template?library_id=%s&id=%s&edit_template=True" % ( self.url, library_id, id ) @@ -897,10 +903,10 @@ tc.fv( '1', 'id', id ) tc.fv( '1', 'set_num_fields', '0' ) tc.fv( '1', 'name', name ) - tc.fv( '1', 'element_name_1', name_1 ) - tc.fv( '1', 'element_description_1', desc_1 ) - tc.fv( '1', 'element_name_2', name_2 ) - tc.fv( '1', 'element_description_2', desc_2 ) + tc.fv( '1', ele_name_1, name_1 ) + tc.fv( '1', ele_desc_1, desc_1 ) + tc.fv( '1', ele_name_2, name_2 ) + tc.fv( '1', ele_desc_2, desc_2 ) tc.submit( 'edit_info_template_button' ) check_str = "Information template '%s' has been updated" % name self.check_page_for_string( check_str ) @@ -988,7 +994,6 @@ for pi in permissions_in: key = '%s_in' % pi url ="%s&%s=%s" % ( url, key, str( role_id ) ) - print url self.home() self.visit_url( "%s/%s" % ( self.url, url ) ) check_str = "Permissions updated for dataset '%s'" % ldda_name @@ -1046,12 +1051,7 @@ dbkey='hg18', message='', check_template_str1='', check_template_str2='', check_template_str3='' ): """Upload new version(s) of a dataset""" self.home() - filename = self.get_filename( filename ) - - url = "%s/admin/library_dataset_dataset_association?upload_option=upload_file&library_id=%s&folder_id=%s&replace_id=%s&message=%s" % \ - ( self.url, library_id, folder_id, library_dataset_id, message ) - print "####url: ", url - + filename = self.get_filename( filename ) self.visit_url( "%s/admin/library_dataset_dataset_association?upload_option=upload_file&library_id=%s&folder_id=%s&replace_id=%s&message=%s" % \ ( self.url, library_id, folder_id, library_dataset_id, message ) ) self.check_page_for_string( 'Upload files' ) diff -r 386e245f8076 -r 48e4b965545b test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Thu May 21 15:48:39 2009 -0400 +++ b/test/functional/test_security_and_libraries.py Tue May 26 14:32:18 2009 -0400 @@ -515,17 +515,30 @@ info_permissions.sort() assert actions == info_permissions, "Permissions for library_item_info id %s not correctly inherited from library %s" \ % ( library_item_info.id, library_one.name ) - # Need the current library_item_info_element.id - last_library_item_info_element_id = galaxy.model.LibraryItemInfoElement.query() \ - .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() - if last_library_item_info_element_id is None: - last_library_item_info_element_id = 0 + element_ids = [] + if library_one.library_info_associations: + # We have a set of LibraryItemInfoElements + last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ + .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() + if not last_library_item_info_element: + element_ids.append( 0 ) + element_ids.append( 1 ) + else: + element_ids.append( last_library_item_info_element.id + 1 ) + element_ids.append( last_library_item_info_element.id + 2 ) + else: + # We only have a set of LibraryItemInfoTemplateElements + for ele in library_one_template.elements: + element_ids.append( ele.id ) + element_ids.sort() # Add information to the library using the template - ele_1_field_name = "info_element_%s_%s" % ( str( library_one_template.id ), str( last_library_item_info_element_id + 1 ) ) + ele_1_field_name = "info_element_%s_%s" % ( str( library_one_template.id ), str( element_ids[0] ) ) ele_1_contents = 'hello' - ele_2_field_name = "info_element_%s_%s" % ( str( library_one_template.id ), str( last_library_item_info_element_id + 2 ) ) + ele_2_field_name = "info_element_%s_%s" % ( str( library_one_template.id ), str( element_ids[1] ) ) ele_2_contents = 'world' - self.edit_library_info( str( library_one.id ), library_one.name, ele_1_field_name, ele_1_contents, ele_2_field_name, ele_2_contents ) + self.edit_library_info( str( library_one.id ), library_one.name, + ele_1_field_name, ele_1_contents, + ele_2_field_name, ele_2_contents ) self.home() self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) self.check_page_for_string( ele_1_contents ) @@ -536,11 +549,17 @@ self.check_page_for_string( ele_2_contents ) # Edit the template new_name = 'Library Template 1 renamed' + new_ele_name_1_field = "element_name_%s" % element_ids[0] new_ele_name_1 = 'wind' + new_ele_desc_1_field = "element_description_%s" % element_ids[0] ele_desc_1 = 'This is the wind component' + new_ele_name_2_field = "element_name_%s" % element_ids[1] new_ele_name_2 = 'bag' + new_ele_desc_2_field = "element_description_%s" % element_ids[1] ele_desc_2 = 'This is the bag component' - self.edit_library_info_template( str( library_one.id ), library_one_template.id, new_name, new_ele_name_1, ele_desc_1, new_ele_name_2, ele_desc_2 ) + self.edit_library_info_template( str( library_one.id ), library_one_template.id, new_name, + new_ele_name_1_field, new_ele_name_1, new_ele_desc_1_field, ele_desc_1, + new_ele_name_2_field, new_ele_name_2, new_ele_desc_2_field, ele_desc_2 ) self.home() self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) self.check_page_for_string( new_ele_name_1 ) @@ -692,20 +711,34 @@ self.home() def test_105_add_template_element( self ): """Testing adding a new element to an existing library template""" + library_one_template.refresh() + element_ids = [] + for ele in library_one_template.elements: + element_ids.append( ele.id ) + element_ids.sort() + name = 'Library Template 1 renamed' + ele_field_name_1 = "element_name_%s" % element_ids[0] ele_name_1 = 'wind' + ele_field_desc_1 = "element_description_%s" % element_ids[0] ele_desc_1 = 'This is the wind component' + ele_field_name_2 = "element_name_%s" % element_ids[1] ele_name_2 = 'bag' + ele_field_desc_2 = "element_description_%s" % element_ids[1] ele_desc_2 = 'This is the bag component' new_ele_name = 'Fubar' new_ele_desc = 'This is the Fubar component' - library_one_template.refresh() + self.add_library_info_template_element( str( library_one.id ), str( library_one_template.id ), library_one_template.name, + ele_field_name_1, ele_name_1, + ele_field_desc_1, ele_desc_1, + ele_field_name_2, ele_name_2, + ele_field_desc_2, ele_desc_2, new_ele_name=new_ele_name, new_ele_desc=new_ele_desc ) @@ -1601,11 +1634,13 @@ self.undelete_role( str( role_two.id ), role_two.name ) def test_270_purge_library( self ): """Testing purging a library""" + self.home() + self.delete_library_item( str( library_one.id ), str( library_one.id ), library_one.name, library_item_type='library' ) self.purge_library( str( library_one.id ), library_one.name ) # Make sure the library was purged library_one.refresh() - if not library_one.purged: - raise AssertionError( 'The library id %s named "%s" has not been marked as purged.' % ( str( library_one.id ), library_one.name ) ) + if not ( library_one.deleted and library_one.purged ): + raise AssertionError( 'The library id %s named "%s" has not been marked as deleted and purged.' % ( str( library_one.id ), library_one.name ) ) def check_folder( library_folder ): for folder in library_folder.folders: folder.refresh() @@ -1635,15 +1670,6 @@ check_folder( library_one.root_folder ) def test_275_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" - ################## - # Eliminate all templates and info associations - ################## - for lia in library_one.library_info_associations: - lia.delete() - lia.flush() - for lita in library_one.library_info_template_associations: - lita.delete() - lita.flush() ################## # Eliminate all non-private roles ##################

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galaxy-dev May 2009