June 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dan: Fixes for SelectToolParameters when changing from an unspecified selection (e.g. Unvalidated) to an existing value.
by Bitbucket 09 Jun '11

09 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d6b048e3483e/ changeset: d6b048e3483e user: dan date: 2011-06-08 23:47:36 summary: Fixes for SelectToolParameters when changing from an unspecified selection (e.g. Unvalidated) to an existing value. affected #: 2 files (233 bytes) --- a/lib/galaxy/datatypes/registry.py Wed Jun 08 17:17:11 2011 -0400 +++ b/lib/galaxy/datatypes/registry.py Wed Jun 08 17:47:36 2011 -0400 @@ -388,9 +388,9 @@ """Returns ( target_ext, existing converted dataset )""" for convert_ext in self.get_converters_by_datatype( dataset.ext ): if isinstance( self.get_datatype_by_extension( convert_ext ), accepted_formats ): - dataset = dataset.get_converted_files_by_type( convert_ext ) - if dataset: - ret_data = dataset + converted_dataset = dataset.get_converted_files_by_type( convert_ext ) + if converted_dataset: + ret_data = converted_dataset elif not converter_safe: continue else: --- a/lib/galaxy/tools/parameters/basic.py Wed Jun 08 17:17:11 2011 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Wed Jun 08 17:47:36 2011 -0400 @@ -603,8 +603,9 @@ # Dynamic options are not yet supported in workflow, allow # specifying the value as text for now. if self.need_late_validation( trans, context ): - assert isinstance( value, UnvalidatedValue ) - value = value.value + if value is not None: + assert isinstance( value, UnvalidatedValue ), "Late validation needed for '%s', but provided value (%s) is not of type UnvalidatedValue (%s)." % ( self.name, value, type( value ) ) + value = value.value if self.multiple: if value is None: value = "" @@ -644,13 +645,11 @@ assert self.multiple, "Multiple values provided but parameter is not expecting multiple values" rval = [] for v in value: - v = util.restore_text( v ) if v not in legal_values: raise ValueError( "An invalid option was selected, please verify" ) rval.append( v ) return rval else: - value = util.restore_text( value ) if value not in legal_values: raise ValueError( "An invalid option was selected, please verify" ) return value @@ -1099,7 +1098,7 @@ # specifying the value as text for now. if self.need_late_validation( trans, other_values ): if value is not None: - assert isinstance( value, UnvalidatedValue ) + assert isinstance( value, UnvalidatedValue ), "Late validation needed for '%s', but provided value (%s) is not of type UnvalidatedValue (%s)." % ( self.name, value, type( value ) ) value = value.value if self.multiple: if value is None: @@ -1127,7 +1126,7 @@ rval = [] for val in value: if val not in self.get_legal_values( trans, other_values ): raise ValueError( "An invalid option was selected, please verify" ) - rval.append( util.restore_text( val ) ) + rval.append( val ) return rval def to_param_dict_string( self, value, other_values={} ): 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: an...@client-75-102-65-120.mobility-up.psu.edu: Patch from Peter Cock (bug534) for cut tool to ignore commented lines.
by Bitbucket 09 Jun '11

09 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b208d252a194/ changeset: b208d252a194 user: an...(a)client-75-102-65-120.mobility-up.psu.edu date: 2011-06-08 23:17:11 summary: Patch from Peter Cock (bug534) for cut tool to ignore commented lines. affected #: 1 file (382 bytes) --- a/tools/filters/cutWrapper.pl Wed Jun 08 16:30:59 2011 -0400 +++ b/tools/filters/cutWrapper.pl Wed Jun 08 17:17:11 2011 -0400 @@ -39,19 +39,38 @@ open (OUT, ">$ARGV[3]") or die "Cannot create $ARGV[2]:$!\n"; open (IN, "<$ARGV[0]") or die "Cannot open $ARGV[0]:$!\n"; -while (<IN>) { - chop; - @in = split /$del/; - foreach $field (@columns) { - if (defined($in[$field-1])) { - push(@out, $in[$field-1]); - } else { - push(@out, "."); - } - } - print OUT join("\t",@out), "\n"; - @out = (); + +while (my $line=<IN>) { + if ($line =~ /^#/) { + #Ignore comment lines + } else { + chop($line); + @in = split(/$del/, $line); + foreach $field (@columns) { + if (defined($in[$field-1])) { + push(@out, $in[$field-1]); + } else { + push(@out, "."); + } + } + print OUT join("\t",@out), "\n"; + @out = (); + } } + +#while (<IN>) { +# chop; +# @in = split /$del/; +# foreach $field (@columns) { +# if (defined($in[$field-1])) { +# push(@out, $in[$field-1]); +# } else { +# push(@out, "."); +# } +# } +# print OUT join("\t",@out), "\n"; +# @out = (); +#} close IN; close OUT; 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: dannon: Fix for bitbucket issue 527, proper inheritance in model for APIItem.
by Bitbucket 08 Jun '11

08 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6f26e35204ab/ changeset: 6f26e35204ab user: dannon date: 2011-06-08 22:30:59 summary: Fix for bitbucket issue 527, proper inheritance in model for APIItem. affected #: 1 file (6 bytes) --- a/lib/galaxy/model/__init__.py Wed Jun 08 16:25:15 2011 -0400 +++ b/lib/galaxy/model/__init__.py Wed Jun 08 16:30:59 2011 -0400 @@ -1106,7 +1106,7 @@ name = unicode( name, 'utf-8' ) return name def get_api_value( self, view='collection' ): - rval = super( APIItem, self ).get_api_value( vew=view ) + rval = super( LibraryFolder, self ).get_api_value( vew=view ) info_association, inherited = self.get_info_association() if info_association: if inherited: 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: an...@client-75-102-65-120.mobility-up.psu.edu: solid2fastq now correctly errors out for out-of-sync solid files. Adderesses user reported bug from yjx@rice.edu
by Bitbucket 08 Jun '11

08 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/80e278c289e4/ changeset: 80e278c289e4 user: an...(a)client-75-102-65-120.mobility-up.psu.edu date: 2011-06-08 22:25:15 summary: solid2fastq now correctly errors out for out-of-sync solid files. Adderesses user reported bug from yjx(a)rice.edu affected #: 3 files (348 bytes) --- a/test-data/solid2fastq_out_2.fastq Wed Jun 08 15:46:20 2011 -0400 +++ b/test-data/solid2fastq_out_2.fastq Wed Jun 08 16:25:15 2011 -0400 @@ -1,1988 +1,1988 @@ @853_7_53/1 -G..1...12.3.023.22.22.2.2..22..2...2222.222.2.2.22. +T..02.1120..22.2..230.22.3..033212.1.1....2221...12 + -!!0!!!10!)!)0)!,-!##!%!%!!##!!'!!!%+&)!%$/!)!$!/(! +!!14!3.15!!47!4!!8+1!$9!(!!,..1)&!3!(!!!!1/9&!!!,3 @853_7_78/1 -G..2...02.2.232.22.11.2.2..12..1...2222.222.2.3.22. +T..13.2222..22.2..222.22.2..222212.2.2....2222...22 + -!!#!!!5,!$!5&+!#8!)#!5!%!!3%!!'!!!$$8+!&)%!)!(!*#! +!!##!###$!!##!&!!#$&!$&!&!!%&)'#'!$!#!!!!&)*(!!!&* @853_7_88/1 -G..3...22.2.032.13.22.2.1..23..0...2130.132.1.2.30. +T..23.2221..13.2..033.30.1..010220.1.2....2222...22 + -!!1!!!42!5!,25!24!77!4!3!!81!!,!!!5147!)/6!,!,!1&! +!!61!5551!!13!4!!.,)!/,!3!!.)/17+!&!5!!!!-'0.!!!,5 @853_7_132/1 -G..2...21.2.200.21.30.1.1..30..0...2112.202.2.0.22. +T..22.2032..32.2..222.22.2..222222.2.2....2222...22 + -!!&!!!5#!)!)&+!2&!',!&!'!!1)!!1!!!4()$!/&,!'!'!0$! 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@853_16_1982/2 -T0331130320230.220330112.210312121022203321222.2302 +G3233..2202.022.00.01.2101.020.2312112223233330.10. + -<88<;9<6<=8;<!;4::8<:@:!>:;;:=6:69===97;9:9>=!=4,< +8789!!:==>!?;<!;>!@8!9><<!>:;!)8:2:6<<:3&64:1,!..! --- a/tools/next_gen_conversion/solid2fastq.py Wed Jun 08 15:46:20 2011 -0400 +++ b/tools/next_gen_conversion/solid2fastq.py Wed Jun 08 16:25:15 2011 -0400 @@ -59,14 +59,19 @@ line = f.readline().rstrip( '\n\r' ) while line.startswith( '#' ): line = f.readline().rstrip( '\n\r' ) - lines.append( line ) + lines.append( line ) + - if lines[0].startswith( '>' ): + if lines[0].startswith( '>' ) and lines[1].startswith( '>' ): + + if lines[0] != lines[1]: + stop_err('Files reads and quality score files are out of sync and likely corrupted. Please, check your input data') + defline = lines[0][1:] if trim_name and ( defline[ len( defline )-3: ] == "_F3" or defline[ len( defline )-3: ] == "_R3" ): defline = defline[ : len( defline )-3 ] - else: + elif ( not lines[0].startswith( '>' ) and not lines[1].startswith( '>' ) and len( lines[0] ) > 0 and len( lines[1] ) > 0 ): if trim_first_base: lines[0] = lines[0][1:] @@ -190,7 +195,7 @@ cur.execute('create index f3_name on f3( name )') cur.execute('create index r3_name on r3( name )') - cur.execute('select * from r3,f3 where f3.name = r3.name') + cur.execute('select * from f3,r3 where f3.name = r3.name') for item in cur: f_out.write( "@%s%s\n%s\n+\n%s\n" % (item[0], "/1", item[1], item[2]) ) r_out.write( "@%s%s\n%s\n+\n%s\n" % (item[3], "/2", item[4], item[5]) ) 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.

1 0

commit/galaxy-central: greg: Fix sample tracking to correctly import samples from a csv file.
by Bitbucket 08 Jun '11

08 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/81a5c317d909/ changeset: 81a5c317d909 user: greg date: 2011-06-08 21:46:20 summary: Fix sample tracking to correctly import samples from a csv file. affected #: 4 files (4.3 KB) --- a/lib/galaxy/web/controllers/requests_common.py Wed Jun 08 15:35:36 2011 -0400 +++ b/lib/galaxy/web/controllers/requests_common.py Wed Jun 08 15:46:20 2011 -0400 @@ -826,7 +826,9 @@ displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd ) if params.get( 'import_samples_button', False ): # Import sample field values from a csv file - return self.__import_samples( trans, cntrller, request, displayable_sample_widgets, libraries, **kwd ) + # TODO: should this be a mapper? + workflows = [ w.latest_workflow for w in trans.user.stored_workflows if not w.deleted ] + return self.__import_samples( trans, cntrller, request, displayable_sample_widgets, libraries, workflows, **kwd ) elif params.get( 'add_sample_button', False ): return self.add_sample( trans, cntrller, request_id, **kwd ) elif params.get( 'save_samples_button', False ): @@ -905,17 +907,17 @@ folder_id=folder_id, **kwd ) history_select_field = self.__build_history_select_field( trans=trans, - user=request.user, - sample_index=len( displayable_sample_widgets ), - history_id=history_id, - **kwd) + user=request.user, + sample_index=len( displayable_sample_widgets ), + history_id=history_id, + **kwd ) workflow_select_field = self.__build_workflow_select_field( trans=trans, - user=request.user, - request=request, - sample_index=len( displayable_sample_widgets ), - workflow_id=workflow_id, - history_id=history_id, - **kwd) + user=request.user, + request=request, + sample_index=len( displayable_sample_widgets ), + workflow_id=workflow_id, + history_id=history_id, + **kwd ) # Append the new sample to the current list of samples for the request displayable_sample_widgets.append( dict( id=None, name=name, @@ -1045,47 +1047,99 @@ transfer_status=transfer_status, message=message, status=status ) - def __import_samples( self, trans, cntrller, request, displayable_sample_widgets, libraries, **kwd ): + def __import_samples( self, trans, cntrller, request, displayable_sample_widgets, libraries, workflows, **kwd ): """ Reads the samples csv file and imports all the samples. The format of the csv file is: - SampleName,DataLibrary,DataLibraryFolder,Field1,Field2.... + SampleName,DataLibraryName,DataLibraryFolderName,HistoryName,WorkflowName,FieldValue1,FieldValue2... """ params = util.Params( kwd ) + current_user_roles = trans.get_current_user_roles() + is_admin = trans.user_is_admin() and cntrller == 'requests_admin' file_obj = params.get( 'file_data', '' ) try: reader = csv.reader( file_obj.file ) for row in reader: library_id = None + library = None folder_id = None - # FIXME: this is bad - what happens when multiple libraries have the same name?? - lib = trans.sa_session.query( trans.model.Library ) \ - .filter( and_( trans.model.Library.table.c.name==row[1], - trans.model.Library.table.c.deleted==False ) ) \ - .first() - if lib: - folder = trans.sa_session.query( trans.model.LibraryFolder ) \ - .filter( and_( trans.model.LibraryFolder.table.c.name==row[2], - trans.model.LibraryFolder.table.c.deleted==False ) ) \ - .first() + folder = None + history_id = None + history = None + workflow_id = None + workflow = None + # Get the library + library = trans.sa_session.query( trans.model.Library ) \ + .filter( and_( trans.model.Library.table.c.name==row[1], + trans.model.Library.table.c.deleted==False ) ) \ + .first() + if library: + # Get the folder + for folder in trans.sa_session.query( trans.model.LibraryFolder ) \ + .filter( and_( trans.model.LibraryFolder.table.c.name==row[2], + trans.model.LibraryFolder.table.c.deleted==False ) ): + if folder.parent_library == library: + break if folder: - library_id = lib.id - folder_id = folder.id + library_id = trans.security.encode_id( library.id ) + folder_id = trans.security.encode_id( folder.id ) library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans, request.user, - len( displayable_sample_widgets ), + len( displayable_sample_widgets ), libraries, None, library_id, folder_id, **kwd ) + # Get the history + history = trans.sa_session.query( trans.model.History ) \ + .filter( and_( trans.model.History.table.c.name==row[3], + trans.model.History.table.c.deleted==False, + trans.model.History.user_id == trans.user.id ) ) \ + .first() + if history: + history_id = trans.security.encode_id( history.id ) + else: + history_id = 'none' + history_select_field = self.__build_history_select_field( trans=trans, + user=request.user, + sample_index=len( displayable_sample_widgets ), + history_id=history_id ) + # Get the workflow + workflow = trans.sa_session.query( trans.model.StoredWorkflow ) \ + .filter( and_( trans.model.StoredWorkflow.table.c.name==row[4], + trans.model.StoredWorkflow.table.c.deleted==False, + trans.model.StoredWorkflow.user_id == trans.user.id ) ) \ + .first() + if workflow: + workflow_id = trans.security.encode_id( workflow.id ) + else: + workflow_id = 'none' + workflow_select_field = self.__build_workflow_select_field( trans=trans, + user=request.user, + request=request, + sample_index=len( displayable_sample_widgets ), + workflow_id=workflow_id, + history_id=history_id ) + field_values = {} + field_names = row[5:] + for field_name in field_names: + field_values[ field_name ] = '' displayable_sample_widgets.append( dict( id=None, - name=row[0], + name=row[0], bar_code='', - library=None, - folder=None, + library=library, + library_id=library_id, library_select_field=library_select_field, + folder=folder, + folder_id=folder_id, folder_select_field=folder_select_field, - field_values=row[3:] ) ) + history=history, + history_id=history_id, + history_select_field=history_select_field, + workflow=workflow, + workflow_id=workflow_id, + workflow_select_field=workflow_select_field, + field_values=field_values ) ) except Exception, e: if str( e ) == "'unicode' object has no attribute 'file'": message = "Select a file" @@ -1488,7 +1542,7 @@ library_select_field=library_select_field, folder_select_field=folder_select_field, history_select_field=history_select_field, - workflow_select_field=workflow_select_field, ) ) + workflow_select_field=workflow_select_field ) ) # There may be additional new samples on the form that have not yet been associated with the request. # TODO: factor this code so it is not duplicating what's above. index = len( samples ) --- a/lib/galaxy/webapps/community/controllers/repository.py Wed Jun 08 15:35:36 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Wed Jun 08 15:46:20 2011 -0400 @@ -269,9 +269,6 @@ category_ids = util.listify( params.get( 'category_id', '' ) ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] if params.get( 'create_repository_button', False ): - # TODOS: - # 1. Make sure we can update the version column in the repository table when new change set are pushed. - # If it's triclky, eliminate the column. error = False message = self.__validate_repository_name( name, trans.user ) if message: --- a/templates/requests/common/add_samples.mako Wed Jun 08 15:35:36 2011 -0400 +++ b/templates/requests/common/add_samples.mako Wed Jun 08 15:46:20 2011 -0400 @@ -61,7 +61,7 @@ <form id="add_samples" name="add_samples" action="${h.url_for( controller='requests_common', action='add_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}" method="post"> %if displayable_sample_widgets: <% - grid_header = '<h3>Add Samples to Sequencing Request "%s"</h3>' % request.name + grid_header = '<h3>Add samples to sequencing request "%s"</h3>' % request.name %> ${render_samples_grid( cntrller, request, displayable_sample_widgets, action='edit_samples', adding_new_samples=True, encoded_selected_sample_ids=[], render_buttons=False, grid_header=grid_header )} <div class="toolParamHelp" style="clear: both;"> @@ -89,8 +89,6 @@ %endif <p/><div class="form-row"> - ## hidden element to make twill work. - ## Greg will fix this <input type="hidden" name="twill" value=""/> %if ( request.samples or displayable_sample_widgets ) and len( displayable_sample_widgets ) > len( request.samples ): <input type="submit" name="add_sample_button" value="Add sample" /> @@ -111,22 +109,19 @@ </div> %if is_unsubmitted: <p/> - ##<div class="toolForm"> - ##<div class="toolFormTitle">Import samples from csv file</div> - <h4><img src="/static/images/silk/resultset_next.png" alt="Hide" onclick="showContent(this);" style="cursor:pointer;"/> Import samples from csv file</h4> - <div style="display:none;"> - <div class="toolFormBody"> - <form id="import" name="import" action="${h.url_for( controller='requests_common', action='add_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}" enctype="multipart/form-data" method="post" > - <div class="form-row"> - <input type="file" name="file_data" /> - <input type="submit" name="import_samples_button" value="Import samples"/> - <div class="toolParamHelp" style="clear: both;"> - The csv file must be in the following format:<br/> - SampleName,DataLibrary,DataLibraryFolder,FieldValue1,FieldValue2... - </div> + <h4><img src="/static/images/silk/resultset_next.png" alt="Hide" onclick="showContent(this);" style="cursor:pointer;"/>Import samples from csv file</h4> + <div style="display:none;"> + <div class="toolFormBody"> + <form id="import" name="import" action="${h.url_for( controller='requests_common', action='add_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}" enctype="multipart/form-data" method="post" > + <div class="form-row"> + <input type="file" name="file_data" /> + <input type="submit" name="import_samples_button" value="Import samples"/> + <div class="toolParamHelp" style="clear: both;"> + The csv file must be in the following format:<br/> + SampleName,DataLibraryName,DataLibraryFolderName,HistoryName,WorkflowName,FieldValue1,FieldValue2... </div> - </form> - </div> + </div> + </form></div> - ##</div> + </div> %endif --- a/test/functional/test_sample_tracking.py Wed Jun 08 15:35:36 2011 -0400 +++ b/test/functional/test_sample_tracking.py Wed Jun 08 15:46:20 2011 -0400 @@ -465,7 +465,7 @@ request_id=self.security.encode_id( request1.id ), sample_value_tuples=sample_value_tuples, folder_options=folder_options, - strings_displayed=[ 'Add Samples to Sequencing Request "%s"' % request1.name, + strings_displayed=[ 'Add samples to sequencing request "%s"' % request1.name, '<input type="text" name="sample_0_name" value="Sample_1" size="10"/>' ], # sample name input field strings_displayed_after_submit=strings_displayed_after_submit ) # check the new sample field values on the request page @@ -704,7 +704,7 @@ self.add_samples( cntrller='requests_admin', request_id=self.security.encode_id( request2.id ), sample_value_tuples=sample_value_tuples, - strings_displayed=[ 'Add Samples to Sequencing Request "%s"' % request2.name, + strings_displayed=[ 'Add samples to sequencing request "%s"' % request2.name, '<input type="text" name="sample_0_name" value="Sample_1" size="10"/>' ], # sample name input field strings_displayed_after_submit=strings_displayed_after_submit ) # Submit the request @@ -869,6 +869,7 @@ sample1_dataset.transfer_status.NOT_STARTED ] self.view_sample_dataset( sample_dataset_id=self.security.encode_id( sample1_dataset.id ), strings_displayed=strings_displayed ) + ''' def test_999_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" # Logged in as admin_user @@ -934,3 +935,4 @@ # Manually delete the group from the database refresh( group ) delete_obj( group ) + ''' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Uploading a compressed library dataset using either the server directory or path paste methods was previously overwriting the input file, which should never happen. This changeset also makes it possible to upload compressed files that remain compressed (by choosing to "link files only"), however, Galaxy does not yet open the compressed file to properly set metadata on its contents.
by Bitbucket 08 Jun '11

08 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2ad3ef1aecc6/ changeset: 2ad3ef1aecc6 user: natefoo date: 2011-06-08 21:35:36 summary: Uploading a compressed library dataset using either the server directory or path paste methods was previously overwriting the input file, which should never happen. This changeset also makes it possible to upload compressed files that remain compressed (by choosing to "link files only"), however, Galaxy does not yet open the compressed file to properly set metadata on its contents. affected #: 1 file (1.1 KB) --- a/tools/data_source/upload.py Wed Jun 08 15:30:40 2011 -0400 +++ b/tools/data_source/upload.py Wed Jun 08 15:35:36 2011 -0400 @@ -129,25 +129,29 @@ file_err( 'The gzipped uploaded file contains inappropriate content', dataset, json_file ) return elif is_gzipped and is_valid: - # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format - CHUNK_SIZE = 2**20 # 1Mb - fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname( dataset.path ), text=False ) - gzipped_file = gzip.GzipFile( dataset.path, 'rb' ) - while 1: - try: - chunk = gzipped_file.read( CHUNK_SIZE ) - except IOError: - os.close( fd ) - os.remove( uncompressed ) - file_err( 'Problem decompressing gzipped data', dataset, json_file ) - return - if not chunk: - break - os.write( fd, chunk ) - os.close( fd ) - gzipped_file.close() - # Replace the gzipped file with the decompressed file - shutil.move( uncompressed, dataset.path ) + if link_data_only == 'copy_files': + # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format + CHUNK_SIZE = 2**20 # 1Mb + fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) + gzipped_file = gzip.GzipFile( dataset.path, 'rb' ) + while 1: + try: + chunk = gzipped_file.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + os.remove( uncompressed ) + file_err( 'Problem decompressing gzipped data', dataset, json_file ) + return + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + gzipped_file.close() + # Replace the gzipped file with the decompressed file if it's safe to do so + if dataset.type in ( 'server_dir', 'path_paste' ): + dataset.path = uncompressed + else: + shutil.move( uncompressed, dataset.path ) dataset.name = dataset.name.rstrip( '.gz' ) data_type = 'gzip' if not data_type and bz2 is not None: @@ -157,78 +161,86 @@ file_err( 'The gzipped uploaded file contains inappropriate content', dataset, json_file ) return elif is_bzipped and is_valid: - # We need to uncompress the temp_name file - CHUNK_SIZE = 2**20 # 1Mb - fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_bunzip2_' % dataset.dataset_id, dir=os.path.dirname( dataset.path ), text=False ) - bzipped_file = bz2.BZ2File( dataset.path, 'rb' ) - while 1: - try: - chunk = bzipped_file.read( CHUNK_SIZE ) - except IOError: - os.close( fd ) - os.remove( uncompressed ) - file_err( 'Problem decompressing bz2 compressed data', dataset, json_file ) - return - if not chunk: - break - os.write( fd, chunk ) - os.close( fd ) - bzipped_file.close() - # Replace the gzipped file with the decompressed file - shutil.move( uncompressed, dataset.path ) + if link_data_only == 'copy_files': + # We need to uncompress the temp_name file + CHUNK_SIZE = 2**20 # 1Mb + fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_bunzip2_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) + bzipped_file = bz2.BZ2File( dataset.path, 'rb' ) + while 1: + try: + chunk = bzipped_file.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + os.remove( uncompressed ) + file_err( 'Problem decompressing bz2 compressed data', dataset, json_file ) + return + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + bzipped_file.close() + # Replace the bzipped file with the decompressed file if it's safe to do so + if dataset.type in ( 'server_dir', 'path_paste' ): + dataset.path = uncompressed + else: + shutil.move( uncompressed, dataset.path ) dataset.name = dataset.name.rstrip( '.bz2' ) data_type = 'bz2' if not data_type: # See if we have a zip archive is_zipped = check_zip( dataset.path ) if is_zipped: - CHUNK_SIZE = 2**20 # 1Mb - uncompressed = None - uncompressed_name = None - unzipped = False - z = zipfile.ZipFile( dataset.path ) - for name in z.namelist(): - if name.endswith('/'): - continue - if unzipped: - stdout = 'ZIP file contained more than one file, only the first file was added to Galaxy.' - break - fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_zip_' % dataset.dataset_id, dir=os.path.dirname( dataset.path ), text=False ) - if sys.version_info[:2] >= ( 2, 6 ): - zipped_file = z.open( name ) - while 1: + if link_data_only == 'copy_files': + CHUNK_SIZE = 2**20 # 1Mb + uncompressed = None + uncompressed_name = None + unzipped = False + z = zipfile.ZipFile( dataset.path ) + for name in z.namelist(): + if name.endswith('/'): + continue + if unzipped: + stdout = 'ZIP file contained more than one file, only the first file was added to Galaxy.' + break + fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_zip_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False ) + if sys.version_info[:2] >= ( 2, 6 ): + zipped_file = z.open( name ) + while 1: + try: + chunk = zipped_file.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + os.remove( uncompressed ) + file_err( 'Problem decompressing zipped data', dataset, json_file ) + return + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + zipped_file.close() + uncompressed_name = name + unzipped = True + else: + # python < 2.5 doesn't have a way to read members in chunks(!) try: - chunk = zipped_file.read( CHUNK_SIZE ) + outfile = open( uncompressed, 'wb' ) + outfile.write( z.read( name ) ) + outfile.close() + uncompressed_name = name + unzipped = True except IOError: os.close( fd ) os.remove( uncompressed ) file_err( 'Problem decompressing zipped data', dataset, json_file ) return - if not chunk: - break - os.write( fd, chunk ) - os.close( fd ) - zipped_file.close() - uncompressed_name = name - unzipped = True - else: - # python < 2.5 doesn't have a way to read members in chunks(!) - try: - outfile = open( uncompressed, 'wb' ) - outfile.write( z.read( name ) ) - outfile.close() - uncompressed_name = name - unzipped = True - except IOError: - os.close( fd ) - os.remove( uncompressed ) - file_err( 'Problem decompressing zipped data', dataset, json_file ) - return - z.close() - # Replace the zipped file with the decompressed file - if uncompressed is not None: - shutil.move( uncompressed, dataset.path ) - dataset.name = uncompressed_name + z.close() + # Replace the zipped file with the decompressed file if it's safe to do so + if uncompressed is not None: + if dataset.type in ( 'server_dir', 'path_paste' ): + dataset.path = uncompressed + else: + shutil.move( uncompressed, dataset.path ) + dataset.name = uncompressed_name data_type = 'zip' if not data_type: if check_binary( dataset.path ): @@ -253,7 +265,7 @@ if data_type != 'binary': if link_data_only == 'copy_files': in_place = True - if dataset.type in ( 'server_dir', 'path_paste' ): + if dataset.type in ( 'server_dir', 'path_paste' ) and data_type not in [ 'gzip', 'bz2', 'zip' ]: in_place = False if dataset.space_to_tab: line_count, converted_path = sniff.convert_newlines_sep2tabs( dataset.path, in_place=in_place ) @@ -277,7 +289,7 @@ '<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> so grooming can be performed.' file_err( err_msg, dataset, json_file ) return - if link_data_only == 'copy_files' and dataset.type in ( 'server_dir', 'path_paste' ): + if link_data_only == 'copy_files' and dataset.type in ( 'server_dir', 'path_paste' ) and data_type not in [ 'gzip', 'bz2', 'zip' ]: # Move the dataset to its "real" path if converted_path is not None: shutil.copy( converted_path, output_path ) @@ -362,7 +374,7 @@ add_file( dataset, registry, json_file, output_path ) # clean up paramfile try: - os.remove( sys.argv[1] ) + os.remove( sys.argv[3] ) except: pass Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: Workflows:
by Bitbucket 08 Jun '11

08 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/92fb946f5c7b/ changeset: 92fb946f5c7b user: kanwei date: 2011-06-08 21:30:40 summary: Workflows: - Fix for postjob rename not escaping quotes. Closes #511 - Tabs->Spaces - Slight reordering to have Save as first option, renamed Layout to Auto Re-layout for clarity affected #: 2 files (210 bytes) --- a/lib/galaxy/jobs/actions/post.py Wed Jun 08 15:16:20 2011 -0400 +++ b/lib/galaxy/jobs/actions/post.py Wed Jun 08 15:30:40 2011 -0400 @@ -10,16 +10,16 @@ if on_output: form = """ if (pja.action_type == "%s"){ - p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'> %s <br/> on " + pja.output_name + "\ - <div style='float: right;' class='buttons'><img src='/static/images/delete_icon.png'></div></div><div class='toolFormBody'>"; + p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'> %s <br/> on " + pja.output_name + "\ + <div style='float: right;' class='buttons'><img src='/static/images/delete_icon.png'></div></div><div class='toolFormBody'>"; %s p_str += "</div><div class='toolParamHelp'>%s</div></div>"; }""" % (action_type, title, content, help) else: - form = """ + form = """ if (pja.action_type == "%s"){ - p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + "</span><div class='toolFormTitle'> %s \ - <div style='float: right;' class='buttons'><img src='/static/images/delete_icon.png'></div></div><div class='toolFormBody'>"; + p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + "</span><div class='toolFormTitle'> %s \ + <div style='float: right;' class='buttons'><img src='/static/images/delete_icon.png'></div></div><div class='toolFormBody'>"; %s p_str += "</div><div class='toolParamHelp'>%s</div></div>"; }""" % (action_type, title, content, help) @@ -75,8 +75,8 @@ @classmethod def get_config_form(cls, trans): form = """ - p_str += "<label for='pja__"+pja.output_name+"__EmailAction'>There are no additional options for this action. You will be emailed upon job completion.</label>\ - <input type='hidden' value='%s' name='pja__"+pja.output_name+"__EmailAction__host'/><input type='hidden' name='pja__"+pja.output_name+"__EmailAction'/>"; + p_str += "<label for='pja__"+pja.output_name+"__EmailAction'>There are no additional options for this action. You will be emailed upon job completion.</label>\ + <input type='hidden' value='%s' name='pja__"+pja.output_name+"__EmailAction__host'/><input type='hidden' name='pja__"+pja.output_name+"__EmailAction'/>"; """ % trans.request.host return get_form_template(cls.name, cls.verbose_name, form, "This action will send an email notifying you when the job is done.", on_output = False) @@ -105,14 +105,14 @@ for dt_name in dtnames: dt_list += """<option id='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype__%s' value='%s'>%s</option>""" % (dt_name, dt_name, dt_name) ps = """ - p_str += "<label for='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype'>New Datatype:</label>\ - <select id='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype' name='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype'>\ - %s\ - </select>"; - if (pja.action_arguments !== undefined && pja.action_arguments.newtype !== undefined){ + p_str += "<label for='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype'>New Datatype:</label>\ + <select id='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype' name='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype'>\ + %s\ + </select>"; + if (pja.action_arguments !== undefined && pja.action_arguments.newtype !== undefined){ p_str += "<scrip" + "t type='text/javascript'>$('#pja__" + pja.output_name + "__ChangeDatatypeAction__newtype').val('" + pja.action_arguments.newtype + "');</scrip" + "t>"; - } - """ % dt_list + } + """ % dt_list # Note the scrip + t hack above. Is there a better way? return get_form_template(cls.name, cls.verbose_name, ps, 'This action will change the datatype of the output to the indicated value.') @@ -140,15 +140,16 @@ @classmethod def get_config_form(cls, trans): form = """ - if ((pja.action_arguments !== undefined) && (pja.action_arguments.newname !== undefined)){ - p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label>\ - <input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value='"+pja.action_arguments.newname + "'/>"; - } - else{ - p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label>\ - <input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value=''/>"; - } - """ + if ((pja.action_arguments !== undefined) && (pja.action_arguments.newname !== undefined)){ + p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label>\ + <input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value=\\"" + pja.action_arguments.newname.replace(/"/g, """) + "\\"/>"; + } + + else{ + p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label>\ + <input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value=''/>"; + } + """ return get_form_template(cls.name, cls.verbose_name, form, "This action will rename the result dataset.") @classmethod @@ -195,8 +196,8 @@ @classmethod def get_config_form(cls, trans): form = """ - p_str += "<label for='pja__"+pja.output_name+"__DeleteDatasetAction'>There are no additional options for this action. This dataset will be marked deleted.</label>\ - <input type='hidden' name='pja__"+pja.output_name+"__DeleteDatasetAction'/>"; + p_str += "<label for='pja__"+pja.output_name+"__DeleteDatasetAction'>There are no additional options for this action. This dataset will be marked deleted.</label>\ + <input type='hidden' name='pja__"+pja.output_name+"__DeleteDatasetAction'/>"; """ return get_form_template(cls.name, cls.verbose_name, form, "This action will rename the result dataset.") --- a/templates/workflow/editor.mako Wed Jun 08 15:16:20 2011 -0400 +++ b/templates/workflow/editor.mako Wed Jun 08 15:30:40 2011 -0400 @@ -242,13 +242,13 @@ }); make_popupmenu( $("#workflow-options-button"), { - ##"Create New" : create_new_workflow_dialog, - "Edit Attributes" : edit_workflow_attributes, + "Save" : save_current_workflow, + ##"Create New" : create_new_workflow_dialog, + "Edit Attributes" : edit_workflow_attributes, ##"Edit Workflow Outputs": edit_workflow_outputs, - "Layout": layout_editor, - "Save" : save_current_workflow, - ##"Load a Workflow" : load_workflow, - "Close": close_editor + "Auto Re-layout": layout_editor, + ##"Load a Workflow" : load_workflow, + "Close": close_editor }); function edit_workflow_outputs(){ @@ -556,8 +556,6 @@ } } - - function show_form_for_tool( text, node ) { $('.right-content').hide(); $("#right-content").show().html( text ); 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: jgoecks: Include post-job actions when importing and exporting workflows. Fixes #518
by Bitbucket 08 Jun '11

08 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/576e78ba4141/ changeset: 576e78ba4141 user: jgoecks date: 2011-06-08 21:16:20 summary: Include post-job actions when importing and exporting workflows. Fixes #518 affected #: 1 file (926 bytes) --- a/lib/galaxy/web/controllers/workflow.py Wed Jun 08 14:41:45 2011 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Wed Jun 08 15:16:20 2011 -0400 @@ -1592,6 +1592,15 @@ 'annotation' : annotation_str } + # Add post-job actions to step dict. + if module.type == 'tool': + pja_dict = {} + for pja in step.post_job_actions: + pja_dict[pja.action_type+pja.output_name] = dict( action_type = pja.action_type, + output_name = pja.output_name, + action_arguments = pja.action_arguments ) + step_dict[ 'post_job_actions' ] = pja_dict + # Data inputs step_dict['inputs'] = [] if module.type == "data_input": @@ -1695,6 +1704,12 @@ if annotation: annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) self.add_item_annotation( trans.sa_session, trans.get_user(), step, annotation ) + # Unpack and add post-job actions. + post_job_actions = step_dict.get( 'post_job_actions', {} ) + for name, pja_dict in post_job_actions.items(): + pja = PostJobAction( pja_dict[ 'action_type' ], + step, pja_dict[ 'output_name' ], + pja_dict[ 'action_arguments' ] ) # Second pass to deal with connections between steps for step in steps: # Input connections 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: 2 new changesets
by Bitbucket 08 Jun '11

08 Jun '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8166f7585484/ changeset: 8166f7585484 user: natefoo date: 2011-06-08 19:25:45 summary: Don't provde the output filename to the upload tool if it's outside Galaxy's files_path, since this means we're only linking data and the output paths are not used (and may contain non-shell-safe characters). Fixes issue #533. affected #: 1 file (299 bytes) --- a/tools/data_source/upload.xml Wed Jun 08 12:46:11 2011 -0400 +++ b/tools/data_source/upload.xml Wed Jun 08 13:25:45 2011 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> -<tool name="Upload File" id="upload1" version="1.1.2"> +<tool name="Upload File" id="upload1" version="1.1.3"><description> from your computer </description> @@ -11,7 +11,12 @@ #while $varExists('output%i' % $outnum): #set $output = $getVar('output%i' % $outnum) #set $outnum += 1 - ${output.dataset.dataset.id}:${output.files_path}:${output} + #set $file_name = $output.file_name + ## FIXME: This is not future-proof for other uses of external_filename (other than for use by the library upload's "link data" feature) + #if $output.dataset.dataset.external_filename: + #set $file_name = "None" + #end if + ${output.dataset.dataset.id}:${output.files_path}:${file_name} #end while </command><inputs nginx_upload="true"> http://bitbucket.org/galaxy/galaxy-central/changeset/b2fa1535d02e/ changeset: b2fa1535d02e user: natefoo date: 2011-06-08 19:26:06 summary: merge. affected #: 6 files (2.7 KB) --- a/lib/galaxy/tools/__init__.py Wed Jun 08 13:25:45 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Wed Jun 08 13:26:06 2011 -0400 @@ -756,13 +756,14 @@ case.inputs = self.parse_input_elem( ElementTree.XML( "<when>%s</when>" % case_inputs ), enctypes, context ) else: - case.inputs = {} + case.inputs = odict() group.cases.append( case ) else: # Should have one child "input" which determines the case input_elem = elem.find( "param" ) assert input_elem is not None, "<conditional> must have a child <param>" group.test_param = self.parse_param_elem( input_elem, enctypes, context ) + possible_cases = list( group.test_param.legal_values ) #store possible cases, undefined whens will have no inputs # Must refresh when test_param changes group.test_param.refresh_on_change = True # And a set of possible cases @@ -771,6 +772,16 @@ case.value = case_elem.get( "value" ) case.inputs = self.parse_input_elem( case_elem, enctypes, context ) group.cases.append( case ) + try: + possible_cases.remove( case.value ) + except: + log.warning( "A when tag has been defined for '%s (%s) --> %s', but does not appear to be selectable." % ( group.name, group.test_param.name, case.value ) ) + for unspecified_case in possible_cases: + log.warning( "A when tag has not been defined for '%s (%s) --> %s', assuming empty inputs." % ( group.name, group.test_param.name, unspecified_case ) ) + case = ConditionalWhen() + case.value = unspecified_case + case.inputs = odict() + group.cases.append( case ) rval[group.name] = group elif elem.tag == "upload_dataset": group = UploadDataset() --- a/lib/galaxy/tools/parameters/basic.py Wed Jun 08 13:25:45 2011 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Wed Jun 08 13:26:06 2011 -0400 @@ -318,7 +318,7 @@ checked = self.checked if value is not None: checked = form_builder.CheckboxField.is_checked( value ) - return form_builder.CheckboxField( self.name, checked ) + return form_builder.CheckboxField( self.name, checked, refresh_on_change = self.refresh_on_change ) def from_html( self, value, trans=None, other_values={} ): return form_builder.CheckboxField.is_checked( value ) def to_python( self, value, app ): @@ -330,6 +330,9 @@ return self.truevalue else: return self.falsevalue + @property + def legal_values( self ): + return [ self.truevalue, self.falsevalue ] class FileToolParameter( ToolParameter ): """ --- a/lib/galaxy/tools/parameters/grouping.py Wed Jun 08 13:25:45 2011 -0400 +++ b/lib/galaxy/tools/parameters/grouping.py Wed Jun 08 13:26:06 2011 -0400 @@ -414,7 +414,10 @@ return "Conditional (%s)" % self.name def get_current_case( self, value, trans ): # Convert value to user representation - str_value = self.test_param.filter_value( value, trans ) + if isinstance( value, bool ): + str_value = self.test_param.to_param_dict_string( value ) + else: + str_value = self.test_param.filter_value( value, trans ) # Find the matching case for index, case in enumerate( self.cases ): if str_value == case.value: --- a/lib/galaxy/web/form_builder.py Wed Jun 08 13:25:45 2011 -0400 +++ b/lib/galaxy/web/form_builder.py Wed Jun 08 13:26:06 2011 -0400 @@ -88,9 +88,17 @@ >>> print CheckboxField( "bar", checked="yes" ).get_html() <input type="checkbox" id="bar" name="bar" value="true" checked="checked"><input type="hidden" name="bar" value="true"> """ - def __init__( self, name, checked=None ): + def __init__( self, name, checked=None, refresh_on_change = False, refresh_on_change_values = None ): self.name = name self.checked = ( checked == True ) or ( isinstance( checked, basestring ) and ( checked.lower() in ( "yes", "true", "on" ) ) ) + self.refresh_on_change = refresh_on_change + self.refresh_on_change_values = refresh_on_change_values or [] + if self.refresh_on_change: + self.refresh_on_change_text = ' refresh_on_change="true" ' + if self.refresh_on_change_values: + self.refresh_on_change_text = '%s refresh_on_change_values="%s" ' % ( self.refresh_on_change_text, ",".join( self.refresh_on_change_values ) ) + else: + self.refresh_on_change_text = '' def get_html( self, prefix="", disabled=False ): if self.checked: checked_text = ' checked="checked"' @@ -102,8 +110,8 @@ # parsing the request, the value 'true' in the hidden field actually means it is NOT checked. # See the is_checked() method below. The prefix is necessary in each case to ensure functional # correctness when the param is inside a conditional. - return '<input type="checkbox" id="%s" name="%s" value="true"%s%s><input type="hidden" name="%s%s" value="true"%s>' \ - % ( id_name, id_name, checked_text, self.get_disabled_str( disabled ), prefix, self.name, self.get_disabled_str( disabled ) ) + return '<input type="checkbox" id="%s" name="%s" value="true"%s%s%s><input type="hidden" name="%s%s" value="true"%s>' \ + % ( id_name, id_name, checked_text, self.get_disabled_str( disabled ), self.refresh_on_change_text, prefix, self.name, self.get_disabled_str( disabled ) ) @staticmethod def is_checked( value ): if value == True: @@ -253,7 +261,7 @@ <div><input type="checkbox" name="bar" value="3" id="bar|3"><label class="inline" for="bar|3">automatic</label></div><div><input type="checkbox" name="bar" value="4" id="bar|4" checked='checked'><label class="inline" for="bar|4">bazooty</label></div> """ - def __init__( self, name, multiple=None, display=None, refresh_on_change=False, refresh_on_change_values=[], size=None ): + def __init__( self, name, multiple=None, display=None, refresh_on_change=False, refresh_on_change_values=None, size=None ): self.name = name self.multiple = multiple or False self.size = size @@ -266,7 +274,7 @@ raise Exception, "Unknown display type: %s" % display self.display = display self.refresh_on_change = refresh_on_change - self.refresh_on_change_values = refresh_on_change_values + self.refresh_on_change_values = refresh_on_change_values or [] if self.refresh_on_change: self.refresh_on_change_text = ' refresh_on_change="true"' if self.refresh_on_change_values: --- a/static/scripts/galaxy.base.js Wed Jun 08 13:25:45 2011 -0400 +++ b/static/scripts/galaxy.base.js Wed Jun 08 13:26:06 2011 -0400 @@ -588,6 +588,23 @@ select_field.get(0).form.submit(); }); + // checkboxes refresh on change + $(":checkbox[refresh_on_change='true']").click( function() { + var select_field = $(this), + select_val = select_field.val(), + refresh = false, + ref_on_change_vals = select_field.attr("refresh_on_change_values"); + if (ref_on_change_vals) { + ref_on_change_vals = ref_on_change_vals.split(','); + var last_selected_value = select_field.attr("last_selected_value"); + if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + return; + } + } + $(window).trigger("refresh_on_change"); + select_field.get(0).form.submit(); + }); + // Links with confirmation $( "a[confirm]" ).click( function() { return confirm( $(this).attr("confirm") ); --- a/static/scripts/packed/galaxy.base.js Wed Jun 08 13:25:45 2011 -0400 +++ b/static/scripts/packed/galaxy.base.js Wed Jun 08 13:26:06 2011 -0400 @@ -1,1 +1,1 @@ -if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return 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a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file +if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function make_popupmenu(b,c){var a=(b.data("menu_options"));b.data("menu_options",c);if(a){return}b.bind("click.show_popup",function(d){$(".popmenu-wrapper").remove();setTimeout(function(){var g=$("<ul id='"+b.attr("id")+"-menu'></ul>");var f=b.data("menu_options");if(obj_length(f)<=0){$("<li>No 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f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:b,minChars:0,hideForLessThanMinChars:false};c.autocomplete(e,f);d.replaceWith(c);var k=function(){var o=c.attr("value");var n=i[o];if(n!==null&&n!==undefined){c.attr("value",n)}else{if(m!==""){c.attr("value",m)}else{c.attr("value","?")}}};c.parents("form").submit(function(){k()});$(document).bind("convert_to_values",function(){k()});if(d.attr("refresh_on_change")=="true"){var h=d.attr("refresh_on_change_values"),l=d.attr("last_selected_value");if(h!==undefined){h=h.split(",")}var j=function(){var n=i[c.attr("value")];if(l!==n&&n!==null&&n!==undefined){if(h!==undefined&&$.inArray(n,h)===-1&&$.inArray(l,h)===-1){return}c.attr("value",n);$(window).trigger("refresh_on_change");c.parents("form").submit()}};c.bind("result",j);c.keyup(function(n){if(n.keyCode===13){j()}});c.keydown(function(n){if(n.keyCode===13){return false}})}})}function 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h=$.jStorage.get("history_expand_state");if(!h){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStorage.set("history_expand_state",h)}).show()};b()}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var 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https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 08 Jun '11

08 Jun '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3d876a5e313b/ changeset: 3d876a5e313b user: dan date: 2011-06-08 19:04:57 summary: Allow conditional statements to not define a 'when' tag for all cases. When a 'when' is not defined, sub-inputs will be empty. Resolves #465. affected #: 1 file (885 bytes) --- a/lib/galaxy/tools/__init__.py Wed Jun 08 12:46:11 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Wed Jun 08 13:04:57 2011 -0400 @@ -756,13 +756,14 @@ case.inputs = self.parse_input_elem( ElementTree.XML( "<when>%s</when>" % case_inputs ), enctypes, context ) else: - case.inputs = {} + case.inputs = odict() group.cases.append( case ) else: # Should have one child "input" which determines the case input_elem = elem.find( "param" ) assert input_elem is not None, "<conditional> must have a child <param>" group.test_param = self.parse_param_elem( input_elem, enctypes, context ) + possible_cases = list( group.test_param.legal_values ) #store possible cases, undefined whens will have no inputs # Must refresh when test_param changes group.test_param.refresh_on_change = True # And a set of possible cases @@ -771,6 +772,16 @@ case.value = case_elem.get( "value" ) case.inputs = self.parse_input_elem( case_elem, enctypes, context ) group.cases.append( case ) + try: + possible_cases.remove( case.value ) + except: + log.warning( "A when tag has been defined for '%s (%s) --> %s', but does not appear to be selectable." % ( group.name, group.test_param.name, case.value ) ) + for unspecified_case in possible_cases: + log.warning( "A when tag has not been defined for '%s (%s) --> %s', assuming empty inputs." % ( group.name, group.test_param.name, unspecified_case ) ) + case = ConditionalWhen() + case.value = unspecified_case + case.inputs = odict() + group.cases.append( case ) rval[group.name] = group elif elem.tag == "upload_dataset": group = UploadDataset() http://bitbucket.org/galaxy/galaxy-central/changeset/91b35c84d7ce/ changeset: 91b35c84d7ce user: dan date: 2011-06-08 19:05:03 summary: Allow boolean inputs (checkbox) to be used as the parameter selector for conditional grouping inputs. Resolves #393. affected #: 5 files (1.9 KB) --- a/lib/galaxy/tools/parameters/basic.py Wed Jun 08 13:04:57 2011 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Wed Jun 08 13:05:03 2011 -0400 @@ -318,7 +318,7 @@ checked = self.checked if value is not None: checked = form_builder.CheckboxField.is_checked( value ) - return form_builder.CheckboxField( self.name, checked ) + return form_builder.CheckboxField( self.name, checked, refresh_on_change = self.refresh_on_change ) def from_html( self, value, trans=None, other_values={} ): return form_builder.CheckboxField.is_checked( value ) def to_python( self, value, app ): @@ -330,6 +330,9 @@ return self.truevalue else: return self.falsevalue + @property + def legal_values( self ): + return [ self.truevalue, self.falsevalue ] class FileToolParameter( ToolParameter ): """ --- a/lib/galaxy/tools/parameters/grouping.py Wed Jun 08 13:04:57 2011 -0400 +++ b/lib/galaxy/tools/parameters/grouping.py Wed Jun 08 13:05:03 2011 -0400 @@ -414,7 +414,10 @@ return "Conditional (%s)" % self.name def get_current_case( self, value, trans ): # Convert value to user representation - str_value = self.test_param.filter_value( value, trans ) + if isinstance( value, bool ): + str_value = self.test_param.to_param_dict_string( value ) + else: + str_value = self.test_param.filter_value( value, trans ) # Find the matching case for index, case in enumerate( self.cases ): if str_value == case.value: --- a/lib/galaxy/web/form_builder.py Wed Jun 08 13:04:57 2011 -0400 +++ b/lib/galaxy/web/form_builder.py Wed Jun 08 13:05:03 2011 -0400 @@ -88,9 +88,17 @@ >>> print CheckboxField( "bar", checked="yes" ).get_html() <input type="checkbox" id="bar" name="bar" value="true" checked="checked"><input type="hidden" name="bar" value="true"> """ - def __init__( self, name, checked=None ): + def __init__( self, name, checked=None, refresh_on_change = False, refresh_on_change_values = None ): self.name = name self.checked = ( checked == True ) or ( isinstance( checked, basestring ) and ( checked.lower() in ( "yes", "true", "on" ) ) ) + self.refresh_on_change = refresh_on_change + self.refresh_on_change_values = refresh_on_change_values or [] + if self.refresh_on_change: + self.refresh_on_change_text = ' refresh_on_change="true" ' + if self.refresh_on_change_values: + self.refresh_on_change_text = '%s refresh_on_change_values="%s" ' % ( self.refresh_on_change_text, ",".join( self.refresh_on_change_values ) ) + else: + self.refresh_on_change_text = '' def get_html( self, prefix="", disabled=False ): if self.checked: checked_text = ' checked="checked"' @@ -102,8 +110,8 @@ # parsing the request, the value 'true' in the hidden field actually means it is NOT checked. # See the is_checked() method below. The prefix is necessary in each case to ensure functional # correctness when the param is inside a conditional. - return '<input type="checkbox" id="%s" name="%s" value="true"%s%s><input type="hidden" name="%s%s" value="true"%s>' \ - % ( id_name, id_name, checked_text, self.get_disabled_str( disabled ), prefix, self.name, self.get_disabled_str( disabled ) ) + return '<input type="checkbox" id="%s" name="%s" value="true"%s%s%s><input type="hidden" name="%s%s" value="true"%s>' \ + % ( id_name, id_name, checked_text, self.get_disabled_str( disabled ), self.refresh_on_change_text, prefix, self.name, self.get_disabled_str( disabled ) ) @staticmethod def is_checked( value ): if value == True: @@ -253,7 +261,7 @@ <div><input type="checkbox" name="bar" value="3" id="bar|3"><label class="inline" for="bar|3">automatic</label></div><div><input type="checkbox" name="bar" value="4" id="bar|4" checked='checked'><label class="inline" for="bar|4">bazooty</label></div> """ - def __init__( self, name, multiple=None, display=None, refresh_on_change=False, refresh_on_change_values=[], size=None ): + def __init__( self, name, multiple=None, display=None, refresh_on_change=False, refresh_on_change_values=None, size=None ): self.name = name self.multiple = multiple or False self.size = size @@ -266,7 +274,7 @@ raise Exception, "Unknown display type: %s" % display self.display = display self.refresh_on_change = refresh_on_change - self.refresh_on_change_values = refresh_on_change_values + self.refresh_on_change_values = refresh_on_change_values or [] if self.refresh_on_change: self.refresh_on_change_text = ' refresh_on_change="true"' if self.refresh_on_change_values: --- a/static/scripts/galaxy.base.js Wed Jun 08 13:04:57 2011 -0400 +++ b/static/scripts/galaxy.base.js Wed Jun 08 13:05:03 2011 -0400 @@ -588,6 +588,23 @@ select_field.get(0).form.submit(); }); + // checkboxes refresh on change + $(":checkbox[refresh_on_change='true']").click( function() { + var select_field = $(this), + select_val = select_field.val(), + refresh = false, + ref_on_change_vals = select_field.attr("refresh_on_change_values"); + if (ref_on_change_vals) { + ref_on_change_vals = ref_on_change_vals.split(','); + var last_selected_value = select_field.attr("last_selected_value"); + if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + return; + } + } + $(window).trigger("refresh_on_change"); + select_field.get(0).form.submit(); + }); + // Links with confirmation $( "a[confirm]" ).click( function() { return confirm( $(this).attr("confirm") ); --- a/static/scripts/packed/galaxy.base.js Wed Jun 08 13:04:57 2011 -0400 +++ b/static/scripts/packed/galaxy.base.js Wed Jun 08 13:05:03 2011 -0400 @@ -1,1 +1,1 @@ -if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return 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c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return 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a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file +if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function make_popupmenu(b,c){var a=(b.data("menu_options"));b.data("menu_options",c);if(a){return}b.bind("click.show_popup",function(d){$(".popmenu-wrapper").remove();setTimeout(function(){var g=$("<ul id='"+b.attr("id")+"-menu'></ul>");var f=b.data("menu_options");if(obj_length(f)<=0){$("<li>No 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f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:b,minChars:0,hideForLessThanMinChars:false};c.autocomplete(e,f);d.replaceWith(c);var k=function(){var o=c.attr("value");var n=i[o];if(n!==null&&n!==undefined){c.attr("value",n)}else{if(m!==""){c.attr("value",m)}else{c.attr("value","?")}}};c.parents("form").submit(function(){k()});$(document).bind("convert_to_values",function(){k()});if(d.attr("refresh_on_change")=="true"){var h=d.attr("refresh_on_change_values"),l=d.attr("last_selected_value");if(h!==undefined){h=h.split(",")}var j=function(){var n=i[c.attr("value")];if(l!==n&&n!==null&&n!==undefined){if(h!==undefined&&$.inArray(n,h)===-1&&$.inArray(l,h)===-1){return}c.attr("value",n);$(window).trigger("refresh_on_change");c.parents("form").submit()}};c.bind("result",j);c.keyup(function(n){if(n.keyCode===13){j()}});c.keydown(function(n){if(n.keyCode===13){return false}})}})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!==""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStorage.get("history_expand_state");if(e){for(var g in e){$("#"+g+" 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