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commit/galaxy-central: greg: Another fix for rendering the contents of a data library - the form to acti on multiple datasets should now be rendered correclty.
by Bitbucket 18 Feb '11

18 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5f5dae7e7ccc/ changeset: r5092:5f5dae7e7ccc user: greg date: 2011-02-18 20:53:35 summary: Another fix for rendering the contents of a data library - the form to acti on multiple datasets should now be rendered correclty. affected #: 1 file (378 bytes) --- a/templates/library/common/browse_library.mako Fri Feb 18 14:46:16 2011 -0500 +++ b/templates/library/common/browse_library.mako Fri Feb 18 14:53:35 2011 -0500 @@ -349,10 +349,6 @@ form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE info_association, inherited = folder.get_info_association( restrict=True ) - - if not self.has_accessible_datasets: - # If we already know the library contains accessible datasets, no need to check again (and we may set it to False if we do). - self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False ) %> %if not root_folder and ( not folder.deleted or show_deleted ): <% encoded_id = trans.security.encode_id(folder.id) %> @@ -489,7 +485,7 @@ info_association, inherited = library.get_info_association() form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE - self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles, search_downward=False ) + self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles ) has_accessible_folders = is_admin or trans.app.security_agent.has_accessible_folders( trans, library.root_folder, trans.user, current_user_roles ) tracked_datasets = {} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: rc: renamed 'samples' to 'sample_widgets' in __save_samples
by Bitbucket 18 Feb '11

18 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6cf34552c6f5/ changeset: r5091:6cf34552c6f5 user: rc date: 2011-02-18 20:46:16 summary: renamed 'samples' to 'sample_widgets' in __save_samples affected #: 1 file (63 bytes) --- a/lib/galaxy/web/controllers/requests_common.py Fri Feb 18 14:34:14 2011 -0500 +++ b/lib/galaxy/web/controllers/requests_common.py Fri Feb 18 14:46:16 2011 -0500 @@ -1093,7 +1093,7 @@ request_widgets=request_widgets, displayable_sample_widgets=displayable_sample_widgets, sample_copy_select_field=sample_copy_select_field ) - def __save_samples( self, trans, cntrller, request, samples, saving_new_samples=False, **kwd ): + def __save_samples( self, trans, cntrller, request, sample_widgets, saving_new_samples=False, **kwd ): # Here we handle saving all new samples added by the user as well as saving # changes to any subset of the request's samples. A sample will not have an # associated SampleState until the request is submitted, at which time the @@ -1109,7 +1109,7 @@ else: redirect_action = 'edit_samples' # Check for duplicate sample names within the request - self.__validate_sample_names( trans, cntrller, request, samples, **kwd ) + self.__validate_sample_names( trans, cntrller, request, sample_widgets, **kwd ) if not saving_new_samples: library = None folder = None @@ -1138,8 +1138,8 @@ # TODO: make changes necessary to just send the samples... encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) # Make sure all samples have a unique bar_code if the state is changing - for sample_index in range( len( samples ) ): - current_sample = samples[ sample_index ] + for sample_index in range( len( sample_widgets ) ): + current_sample = sample_widgets[ sample_index ] if current_sample is None: # We have a None value because the user did not select this sample # on which to perform the action. @@ -1163,15 +1163,15 @@ library_id = params.get( 'sample_operation_library_id', 'none' ) folder_id = params.get( 'sample_operation_folder_id', 'none' ) library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) - for sample_index in range( len( samples ) ): - current_sample = samples[ sample_index ] + for sample_index in range( len( sample_widgets ) ): + current_sample = sample_widgets[ sample_index ] if current_sample is None: # We have a None value because the user did not select this sample # on which to perform the action. continue current_sample[ 'library' ] = library current_sample[ 'folder' ] = folder - self.__update_samples( trans, cntrller, request, samples, **kwd ) + self.__update_samples( trans, cntrller, request, sample_widgets, **kwd ) message = 'Changes made to the samples have been saved. ' else: # Saving a newly created sample. The sample will not have an associated SampleState @@ -1179,9 +1179,9 @@ # set to the first SampleState configured for the request's RequestType configured # by the admin ( i.e., the sample's SampleState would be set to request.type.states[0] ). new_samples = [] - for index in range( len( samples ) - len( request.samples ) ): + for index in range( len( sample_widgets ) - len( request.samples ) ): sample_index = len( request.samples ) - sample_widget = samples[ sample_index ] + sample_widget = sample_widgets[ sample_index ] form_values = trans.model.FormValues( request.type.sample_form, sample_widget[ 'field_values' ] ) trans.sa_session.add( form_values ) trans.sa_session.flush() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Remove the new/ subdirectory from the eggs repository and update the pysam egg.
by Bitbucket 18 Feb '11

18 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/41b368b104ff/ changeset: r5090:41b368b104ff user: natefoo date: 2011-02-18 20:34:14 summary: Remove the new/ subdirectory from the eggs repository and update the pysam egg. affected #: 2 files (5 bytes) --- a/dist-eggs.ini Fri Feb 18 13:22:31 2011 -0500 +++ b/dist-eggs.ini Fri Feb 18 14:34:14 2011 -0500 @@ -22,7 +22,7 @@ py2.4-macosx-10.3-fat-ucs2 = lonnie.bx.psu.edu /usr/local/bin/python2.4 py2.5-macosx-10.3-fat-ucs2 = lonnie.bx.psu.edu /usr/local/bin/python2.5 py2.6-macosx-10.3-fat-ucs2 = lonnie.bx.psu.edu /usr/local/bin/python2.6 -py2.6-macosx-10.6-universal-ucs2 = bach.bx.psu.edu /usr/bin/python2.6 +py2.6-macosx-10.6-universal-ucs2 = fanty.bx.psu.edu /usr/bin/python2.6 py2.4-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.4 py2.5-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.5 py2.6-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.6 --- a/eggs.ini Fri Feb 18 13:22:31 2011 -0500 +++ b/eggs.ini Fri Feb 18 14:34:14 2011 -0500 @@ -7,7 +7,7 @@ ; [general] -repository = http://eggs.g2.bx.psu.edu/new +repository = http://eggs.g2.bx.psu.edu ; these eggs must be scrambled for your local environment no_auto = pbs_python DRMAA_python @@ -69,7 +69,7 @@ bx_python = _14b6a6c95da6 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0 SQLAlchemy = _dev_r6498 -pysam = _kanwei_a92c29d5cdec +pysam = _kanwei_ae2bd50d9945 ; dependency source urls, necessary for scrambling. for an explanation, see ; the wiki page above Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Don't copy ez_setup.py to egg build directories anymore, and provide a more useful error message when an egg is missing a dependency with a version conflict.
by Bitbucket 18 Feb '11

18 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c8f8f80902d1/ changeset: r5089:c8f8f80902d1 user: natefoo date: 2011-02-18 19:22:31 summary: Don't copy ez_setup.py to egg build directories anymore, and provide a more useful error message when an egg is missing a dependency with a version conflict. affected #: 2 files (427 bytes) --- a/lib/galaxy/eggs/__init__.py Fri Feb 18 12:07:27 2011 -0500 +++ b/lib/galaxy/eggs/__init__.py Fri Feb 18 13:22:31 2011 -0500 @@ -187,6 +187,10 @@ else: raise EggNotFetchable( self ) except pkg_resources.VersionConflict, e: + if e.args[1].key != e.args[0].key: + log.error( "One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution." ) + log.error( 'Dependency "%s" requires "%s"' % ( e.args[0].project_name, str( e.args[1] ) ) ) + raise # there's a conflicting egg on the path, remove it return self.version_conflict( e.args[0], e.args[1] ) def version_conflict( self, conflict_dist, conflict_req ): --- a/lib/galaxy/eggs/scramble.py Fri Feb 18 12:07:27 2011 -0500 +++ b/lib/galaxy/eggs/scramble.py Fri Feb 18 13:22:31 2011 -0500 @@ -54,7 +54,6 @@ self.copy_build_script() if not os.path.exists( ScrambleEgg.ez_setup ): URLRetriever().retrieve( ScrambleEgg.ez_setup_url, ScrambleEgg.ez_setup ) - shutil.copyfile( ScrambleEgg.ez_setup, os.path.join( self.buildpath, 'ez_setup.py' ) ) self.run_scramble_script() new_egg = os.path.join( self.buildpath, 'dist', os.path.basename( self.distribution.location ) ) if not os.path.exists( new_egg ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Do not print summary information in FASTQ groomer when grooming an empty file.
by Bitbucket 18 Feb '11

18 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2af990906c8f/ changeset: r5088:2af990906c8f user: dan date: 2011-02-18 18:07:27 summary: Do not print summary information in FASTQ groomer when grooming an empty file. affected #: 2 files (168 bytes) --- a/lib/galaxy_utils/sequence/fastq.py Fri Feb 18 12:04:26 2011 -0500 +++ b/lib/galaxy_utils/sequence/fastq.py Fri Feb 18 12:07:27 2011 -0500 @@ -314,8 +314,12 @@ rval.append( fastq_format ) return rval def get_ascii_range( self ): + if not self.ascii_values_used: + return None return ( min( self.ascii_values_used ), max( self.ascii_values_used ) ) def get_decimal_range( self ): + if not self.nuc_index_quality: + return None decimal_values_used = [] for scores in self.nuc_index_quality: decimal_values_used.extend( scores.keys() ) --- a/tools/fastq/fastq_groomer.py Fri Feb 18 12:04:26 2011 -0500 +++ b/tools/fastq/fastq_groomer.py Fri Feb 18 12:07:27 2011 -0500 @@ -23,15 +23,16 @@ if read_count is not None: print "Groomed %i %s reads into %s reads." % ( read_count + 1, input_type, output_type ) + if input_type != output_type and 'solexa' in [ input_type, output_type ]: + print "Converted between Solexa and PHRED scores." + if summarize_input: + print "Based upon quality and sequence, the input data is valid for: %s" % ( ", ".join( aggregator.get_valid_formats() ) or "None" ) + ascii_range = aggregator.get_ascii_range() + decimal_range = aggregator.get_decimal_range() + print "Input ASCII range: %s(%i) - %s(%i)" % ( repr( ascii_range[0] ), ord( ascii_range[0] ), repr( ascii_range[1] ), ord( ascii_range[1] ) ) #print using repr, since \x00 (null) causes info truncation in galaxy when printed + print "Input decimal range: %i - %i" % ( decimal_range[0], decimal_range[1] ) else: print "No valid FASTQ reads were provided." - if input_type != output_type and 'solexa' in [ input_type, output_type ]: - print "Converted between Solexa and PHRED scores." - if summarize_input: - print "Based upon quality and sequence, the input data is valid for: %s" % ( ", ".join( aggregator.get_valid_formats() ) or "None" ) - ascii_range = aggregator.get_ascii_range() - decimal_range = aggregator.get_decimal_range() - print "Input ASCII range: %s(%i) - %s(%i)" % ( repr( ascii_range[0] ), ord( ascii_range[0] ), repr( ascii_range[1] ), ord( ascii_range[1] ) ) #print using repr, since \x00 (null) causes info truncation in galaxy when printed - print "Input decimal range: %i - %i" % ( decimal_range[0], decimal_range[1] ) -if __name__ == "__main__": main() \ No newline at end of file + +if __name__ == "__main__": main() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for changing the selected data library and folder for a checked list of samples ( a subset of the entire list of the request's samples ).
by Bitbucket 18 Feb '11

18 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c0f7d67ece33/ changeset: r5087:c0f7d67ece33 user: greg date: 2011-02-18 18:04:26 summary: Fix for changing the selected data library and folder for a checked list of samples ( a subset of the entire list of the request's samples ). affected #: 1 file (1.0 KB) --- a/lib/galaxy/web/controllers/requests_common.py Fri Feb 18 11:18:52 2011 -0500 +++ b/lib/galaxy/web/controllers/requests_common.py Fri Feb 18 12:04:26 2011 -0500 @@ -463,8 +463,18 @@ samples.append( sample ) else: samples.append( None ) - # The __save_samples method requires sample_widgets, not sample objects - sample_widgets = self.__get_sample_widgets( trans, request, samples, **kwd ) + # The __save_samples method requires sample_widgets, not sample objects, so we'll get what we + # need by calling __get_sample_widgets(). However, we need to take care here because __get_sample_widgets() + # is used to populate the sample widget dicts from kwd, and the method assumes that a None object in the + # received list of samples should be populated from the db. Since we're just re-using the method here to + # change our list of samples into a list of sample widgets, we'll need to make sure to keep track of our + # None objects. + sample_widgets = [ obj for obj in samples ] + sample_widgets = self.__get_sample_widgets( trans, request, sample_widgets, **kwd ) + # Replace each sample widget dict with a None object if necessary + for index, obj in enumerate( samples ): + if obj is None: + sample_widgets[ index ] = None else: sample_widgets = displayable_sample_widgets return self.__save_samples( trans, cntrller, request, sample_widgets, saving_new_samples=False, **kwd ) @@ -1155,6 +1165,10 @@ library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) for sample_index in range( len( samples ) ): current_sample = samples[ sample_index ] + if current_sample is None: + # We have a None value because the user did not select this sample + # on which to perform the action. + continue current_sample[ 'library' ] = library current_sample[ 'folder' ] = folder self.__update_samples( trans, cntrller, request, samples, **kwd ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: rc: Backed out of changeset 5085:0ce482e2ec78
by Bitbucket 18 Feb '11

18 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0320a5b0d1a7/ changeset: r5086:0320a5b0d1a7 user: rc date: 2011-02-18 17:18:52 summary: Backed out of changeset 5085:0ce482e2ec78 affected #: 1 file (244 bytes) --- a/lib/galaxy/web/controllers/requests_common.py Fri Feb 18 10:49:46 2011 -0500 +++ b/lib/galaxy/web/controllers/requests_common.py Fri Feb 18 11:18:52 2011 -0500 @@ -445,7 +445,6 @@ kwd[ 'message' ] = message handle_error( **kwd ) if params.get( 'save_samples_button', False ): - samples = [] if encoded_selected_sample_ids: # We need the list of displayable_sample_widgets to include the same number # of objects that that request.samples has so that we can enumerate over each @@ -453,6 +452,7 @@ # used the multi-select check boxes when editing sample widgets, but didn't # select all of them. We'll first get the set of samples corresponding to the # checked sample ids. + samples = [] selected_samples = [] for encoded_sample_id in encoded_selected_sample_ids: sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( encoded_sample_id ) ) @@ -467,7 +467,7 @@ sample_widgets = self.__get_sample_widgets( trans, request, samples, **kwd ) else: sample_widgets = displayable_sample_widgets - return self.__save_samples( trans, cntrller, request, samples, sample_widgets, saving_new_samples=False, **kwd ) + return self.__save_samples( trans, cntrller, request, sample_widgets, saving_new_samples=False, **kwd ) request_widgets = self.__get_request_widgets( trans, request.id ) sample_copy_select_field = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) libraries_select_field, folders_select_field = self.__build_library_and_folder_select_fields( trans, @@ -806,8 +806,7 @@ elif params.get( 'add_sample_button', False ): return self.add_sample( trans, cntrller, request_id, **kwd ) elif params.get( 'save_samples_button', False ): - samples = [] - return self.__save_samples( trans, cntrller, request, samples, displayable_sample_widgets, saving_new_samples=True, **kwd ) + return self.__save_samples( trans, cntrller, request, displayable_sample_widgets, saving_new_samples=True, **kwd ) request_widgets = self.__get_request_widgets( trans, request.id ) sample_copy_select_field = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) libraries_select_field, folders_select_field = self.__build_library_and_folder_select_fields( trans, @@ -1084,7 +1083,7 @@ request_widgets=request_widgets, displayable_sample_widgets=displayable_sample_widgets, sample_copy_select_field=sample_copy_select_field ) - def __save_samples( self, trans, cntrller, request, samples, sample_widgets, saving_new_samples=False, **kwd ): + def __save_samples( self, trans, cntrller, request, samples, saving_new_samples=False, **kwd ): # Here we handle saving all new samples added by the user as well as saving # changes to any subset of the request's samples. A sample will not have an # associated SampleState until the request is submitted, at which time the @@ -1100,7 +1099,7 @@ else: redirect_action = 'edit_samples' # Check for duplicate sample names within the request - self.__validate_sample_names( trans, cntrller, request, sample_widgets, **kwd ) + self.__validate_sample_names( trans, cntrller, request, samples, **kwd ) if not saving_new_samples: library = None folder = None @@ -1129,16 +1128,17 @@ # TODO: make changes necessary to just send the samples... encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) # Make sure all samples have a unique bar_code if the state is changing - for sample_index, sample in enumerate( samples ): - if sample is None: + for sample_index in range( len( samples ) ): + current_sample = samples[ sample_index ] + if current_sample is None: # We have a None value because the user did not select this sample # on which to perform the action. continue - current_sample = sample_widgets[ sample_index ] + request_sample = request.samples[ sample_index ] bar_code = current_sample[ 'bar_code' ] if bar_code: # If the sample has a new bar_code, make sure it is unique. - bc_message = self.__validate_bar_code( trans, sample, bar_code ) + bc_message = self.__validate_bar_code( trans, request_sample, bar_code ) if bc_message: message += bc_message kwd[ 'message' ] = message @@ -1153,15 +1153,11 @@ library_id = params.get( 'sample_operation_library_id', 'none' ) folder_id = params.get( 'sample_operation_folder_id', 'none' ) library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) - for sample_index, sample in enumerate( samples ): - if sample is None: - # We have a None value because the user did not select this sample - # on which to perform the action. - continue - current_sample = sample_widgets[ sample_index ] + for sample_index in range( len( samples ) ): + current_sample = samples[ sample_index ] current_sample[ 'library' ] = library current_sample[ 'folder' ] = folder - self.__update_samples( trans, cntrller, request, sample_widgets, **kwd ) + self.__update_samples( trans, cntrller, request, samples, **kwd ) message = 'Changes made to the samples have been saved. ' else: # Saving a newly created sample. The sample will not have an associated SampleState @@ -1169,9 +1165,9 @@ # set to the first SampleState configured for the request's RequestType configured # by the admin ( i.e., the sample's SampleState would be set to request.type.states[0] ). new_samples = [] - for index in range( len( sample_widgets ) - len( request.samples ) ): + for index in range( len( samples ) - len( request.samples ) ): sample_index = len( request.samples ) - sample_widget = sample_widgets[ sample_index ] + sample_widget = samples[ sample_index ] form_values = trans.model.FormValues( request.type.sample_form, sample_widget[ 'field_values' ] ) trans.sa_session.add( form_values ) trans.sa_session.flush() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: rc: bug fix: bulk operations on samples for changing target data libraries was broken
by Bitbucket 18 Feb '11

18 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0ce482e2ec78/ changeset: r5085:0ce482e2ec78 user: rc date: 2011-02-18 16:49:46 summary: bug fix: bulk operations on samples for changing target data libraries was broken affected #: 1 file (244 bytes) --- a/lib/galaxy/web/controllers/requests_common.py Fri Feb 18 10:42:13 2011 -0500 +++ b/lib/galaxy/web/controllers/requests_common.py Fri Feb 18 10:49:46 2011 -0500 @@ -445,6 +445,7 @@ kwd[ 'message' ] = message handle_error( **kwd ) if params.get( 'save_samples_button', False ): + samples = [] if encoded_selected_sample_ids: # We need the list of displayable_sample_widgets to include the same number # of objects that that request.samples has so that we can enumerate over each @@ -452,7 +453,6 @@ # used the multi-select check boxes when editing sample widgets, but didn't # select all of them. We'll first get the set of samples corresponding to the # checked sample ids. - samples = [] selected_samples = [] for encoded_sample_id in encoded_selected_sample_ids: sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( encoded_sample_id ) ) @@ -467,7 +467,7 @@ sample_widgets = self.__get_sample_widgets( trans, request, samples, **kwd ) else: sample_widgets = displayable_sample_widgets - return self.__save_samples( trans, cntrller, request, sample_widgets, saving_new_samples=False, **kwd ) + return self.__save_samples( trans, cntrller, request, samples, sample_widgets, saving_new_samples=False, **kwd ) request_widgets = self.__get_request_widgets( trans, request.id ) sample_copy_select_field = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) libraries_select_field, folders_select_field = self.__build_library_and_folder_select_fields( trans, @@ -806,7 +806,8 @@ elif params.get( 'add_sample_button', False ): return self.add_sample( trans, cntrller, request_id, **kwd ) elif params.get( 'save_samples_button', False ): - return self.__save_samples( trans, cntrller, request, displayable_sample_widgets, saving_new_samples=True, **kwd ) + samples = [] + return self.__save_samples( trans, cntrller, request, samples, displayable_sample_widgets, saving_new_samples=True, **kwd ) request_widgets = self.__get_request_widgets( trans, request.id ) sample_copy_select_field = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) libraries_select_field, folders_select_field = self.__build_library_and_folder_select_fields( trans, @@ -1083,7 +1084,7 @@ request_widgets=request_widgets, displayable_sample_widgets=displayable_sample_widgets, sample_copy_select_field=sample_copy_select_field ) - def __save_samples( self, trans, cntrller, request, samples, saving_new_samples=False, **kwd ): + def __save_samples( self, trans, cntrller, request, samples, sample_widgets, saving_new_samples=False, **kwd ): # Here we handle saving all new samples added by the user as well as saving # changes to any subset of the request's samples. A sample will not have an # associated SampleState until the request is submitted, at which time the @@ -1099,7 +1100,7 @@ else: redirect_action = 'edit_samples' # Check for duplicate sample names within the request - self.__validate_sample_names( trans, cntrller, request, samples, **kwd ) + self.__validate_sample_names( trans, cntrller, request, sample_widgets, **kwd ) if not saving_new_samples: library = None folder = None @@ -1128,17 +1129,16 @@ # TODO: make changes necessary to just send the samples... encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) # Make sure all samples have a unique bar_code if the state is changing - for sample_index in range( len( samples ) ): - current_sample = samples[ sample_index ] - if current_sample is None: + for sample_index, sample in enumerate( samples ): + if sample is None: # We have a None value because the user did not select this sample # on which to perform the action. continue - request_sample = request.samples[ sample_index ] + current_sample = sample_widgets[ sample_index ] bar_code = current_sample[ 'bar_code' ] if bar_code: # If the sample has a new bar_code, make sure it is unique. - bc_message = self.__validate_bar_code( trans, request_sample, bar_code ) + bc_message = self.__validate_bar_code( trans, sample, bar_code ) if bc_message: message += bc_message kwd[ 'message' ] = message @@ -1153,11 +1153,15 @@ library_id = params.get( 'sample_operation_library_id', 'none' ) folder_id = params.get( 'sample_operation_folder_id', 'none' ) library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) - for sample_index in range( len( samples ) ): - current_sample = samples[ sample_index ] + for sample_index, sample in enumerate( samples ): + if sample is None: + # We have a None value because the user did not select this sample + # on which to perform the action. + continue + current_sample = sample_widgets[ sample_index ] current_sample[ 'library' ] = library current_sample[ 'folder' ] = folder - self.__update_samples( trans, cntrller, request, samples, **kwd ) + self.__update_samples( trans, cntrller, request, sample_widgets, **kwd ) message = 'Changes made to the samples have been saved. ' else: # Saving a newly created sample. The sample will not have an associated SampleState @@ -1165,9 +1169,9 @@ # set to the first SampleState configured for the request's RequestType configured # by the admin ( i.e., the sample's SampleState would be set to request.type.states[0] ). new_samples = [] - for index in range( len( samples ) - len( request.samples ) ): + for index in range( len( sample_widgets ) - len( request.samples ) ): sample_index = len( request.samples ) - sample_widget = samples[ sample_index ] + sample_widget = sample_widgets[ sample_index ] form_values = trans.model.FormValues( request.type.sample_form, sample_widget[ 'field_values' ] ) trans.sa_session.add( form_values ) trans.sa_session.flush() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix typo in Intersect tool description.
by Bitbucket 18 Feb '11

18 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e7bc439ef1dd/ changeset: r5084:e7bc439ef1dd user: dan date: 2011-02-18 16:42:13 summary: Fix typo in Intersect tool description. affected #: 1 file (0 bytes) --- a/tools/new_operations/intersect.xml Thu Feb 17 17:21:54 2011 -0500 +++ b/tools/new_operations/intersect.xml Fri Feb 18 10:42:13 2011 -0500 @@ -1,5 +1,5 @@ <tool id="gops_intersect_1" name="Intersect"> - <description>the intervals of two datastes</description> + <description>the intervals of two datasets</description><command interpreter="python">gops_intersect.py $input1 $input2 $output Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: Update pysam egg to 0.4.1
by Bitbucket 17 Feb '11

17 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5fa0593cd83c/ changeset: r5083:5fa0593cd83c user: kanwei date: 2011-02-17 23:21:54 summary: Update pysam egg to 0.4.1 affected #: 1 file (0 bytes) --- a/eggs.ini Thu Feb 17 15:35:07 2011 -0500 +++ b/eggs.ini Thu Feb 17 17:21:54 2011 -0500 @@ -21,7 +21,7 @@ pbs_python = 4.1.0 psycopg2 = 2.0.13 pycrypto = 2.0.1 -pysam = 0.1.1 +pysam = 0.4.1 pysqlite = 2.5.6 python_lzo = 1.08_2.03_static simplejson = 2.1.1 @@ -69,7 +69,7 @@ bx_python = _14b6a6c95da6 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0 SQLAlchemy = _dev_r6498 -pysam = _kanwei_90e03180969d +pysam = _kanwei_a92c29d5cdec ; dependency source urls, necessary for scrambling. for an explanation, see ; the wiki page above Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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