November 2009 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2960: Fix maf_utilities.src_split. Should resolve ti...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/91a3bbb52d7a changeset: 2960:91a3bbb52d7a user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Nov 04 12:15:53 2009 -0500 description: Fix maf_utilities.src_split. Should resolve tickets #200, #215 and #220. Note: Do not use bx.align.src_split in Galaxy. diffstat: lib/galaxy/datatypes/converters/maf_to_interval_converter.py | 2 +- lib/galaxy/datatypes/converters/maf_to_interval_converter.xml | 2 +- lib/galaxy/tools/util/maf_utilities.py | 11 +++++++---- 3 files changed, 9 insertions(+), 6 deletions(-) diffs (49 lines): diff -r 4bca8f8ed94d -r 91a3bbb52d7a lib/galaxy/datatypes/converters/maf_to_interval_converter.py --- a/lib/galaxy/datatypes/converters/maf_to_interval_converter.py Wed Nov 04 11:35:50 2009 -0500 +++ b/lib/galaxy/datatypes/converters/maf_to_interval_converter.py Wed Nov 04 12:15:53 2009 -0500 @@ -21,7 +21,7 @@ for block in bx.align.maf.Reader( open( input_name, 'r' ) ): for c in maf_utilities.iter_components_by_src_start( block, species ): if c is not None: - out.write( "%s\t%i\t%i\t%s\n" % ( bx.align.src_split( c.src )[-1], c.get_forward_strand_start(), c.get_forward_strand_end(), c.strand ) ) + out.write( "%s\t%i\t%i\t%s\n" % ( maf_utilities.src_split( c.src )[-1], c.get_forward_strand_start(), c.get_forward_strand_end(), c.strand ) ) count += 1 except Exception, e: print >> sys.stderr, "There was a problem processing your input: %s" % e diff -r 4bca8f8ed94d -r 91a3bbb52d7a lib/galaxy/datatypes/converters/maf_to_interval_converter.xml --- a/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml Wed Nov 04 11:35:50 2009 -0500 +++ b/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml Wed Nov 04 12:15:53 2009 -0500 @@ -1,4 +1,4 @@ -<tool id="CONVERTER_maf_to_interval_0" name="Convert MAF to Genomic Intervals" version="1.0.1"> +<tool id="CONVERTER_maf_to_interval_0" name="Convert MAF to Genomic Intervals" version="1.0.2">  <command interpreter="python">maf_to_interval_converter.py $output1 $input1 ${input1.metadata.dbkey}</command> <inputs> diff -r 4bca8f8ed94d -r 91a3bbb52d7a lib/galaxy/tools/util/maf_utilities.py --- a/lib/galaxy/tools/util/maf_utilities.py Wed Nov 04 11:35:50 2009 -0500 +++ b/lib/galaxy/tools/util/maf_utilities.py Wed Nov 04 12:15:53 2009 -0500 @@ -20,9 +20,12 @@ SRC_SPLIT_CHAR = '.' def src_split( src ): - spec, chrom = bx.align.maf.src_split( src ) - if None in [ spec, chrom ]: - spec = chrom = src + fields = src.split( SRC_SPLIT_CHAR, 1 ) + spec = fields.pop( 0 ) + if fields: + chrom = fields + else: + chrom = spec return spec, chrom def src_merge( spec, chrom, contig = None ): @@ -530,7 +533,7 @@ if suffix: header = "%s%s" % ( header, suffix ) else: - header = "%s%s" % ( header, bx.align.src_split( component.src )[ 0 ] ) + header = "%s%s" % ( header, src_split( component.src )[ 0 ] ) return header def get_attributes_from_fasta_header( header ):

1 0

[hg] galaxy 2958: Fixed the ordering in selectboxes
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0e78d558fe57 changeset: 2958:0e78d558fe57 user: rc date: Wed Nov 04 10:16:20 2009 -0500 description: Fixed the ordering in selectboxes Fixed a bug in editing samples in the request page diffstat: lib/galaxy/model/mapping.py | 3 ++- lib/galaxy/web/controllers/forms.py | 4 +++- lib/galaxy/web/controllers/requests.py | 9 +++++---- lib/galaxy/web/controllers/requests_admin.py | 22 ++++++++++++---------- templates/admin/requests/show_request.mako | 2 +- templates/requests/show_request.mako | 4 ---- test/base/twilltestcase.py | 2 +- 7 files changed, 24 insertions(+), 22 deletions(-) diffs (191 lines): diff -r 5b2d593d9aed -r 0e78d558fe57 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Wed Nov 04 10:04:51 2009 -0500 +++ b/lib/galaxy/model/mapping.py Wed Nov 04 10:16:20 2009 -0500 @@ -652,7 +652,8 @@ primaryjoin=( Request.table.c.user_id == User.table.c.id ), backref="requests" ), samples=relation( Sample, - primaryjoin=( Request.table.c.id == Sample.table.c.request_id ) ), + primaryjoin=( Request.table.c.id == Sample.table.c.request_id ), + order_by=asc(Sample.table.c.update_time) ), folder=relation( LibraryFolder, primaryjoin=( Request.table.c.folder_id == LibraryFolder.table.c.id ) ), library=relation( Library, diff -r 5b2d593d9aed -r 0e78d558fe57 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Wed Nov 04 10:04:51 2009 -0500 +++ b/lib/galaxy/web/controllers/forms.py Wed Nov 04 10:16:20 2009 -0500 @@ -60,7 +60,9 @@ form_type_selectbox.add_option('Select one', 'none', selected=True) else: form_type_selectbox.add_option('Select one', 'none') - for ft in trans.app.model.FormDefinition.types.items(): + fd_types = trans.app.model.FormDefinition.types.items() + fd_types.sort() + for ft in fd_types: if selected == ft[1]: form_type_selectbox.add_option(ft[1], ft[1], selected=True) else: diff -r 5b2d593d9aed -r 0e78d558fe57 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Wed Nov 04 10:04:51 2009 -0500 +++ b/lib/galaxy/web/controllers/requests.py Wed Nov 04 10:16:20 2009 -0500 @@ -304,8 +304,7 @@ s = trans.app.model.Sample(sample_name, '', request, form_values) s.flush() else: - for index in range(len(current_samples)): - sample_index = index + for sample_index in range(len(current_samples)): sample_name = current_samples[sample_index][0] new_sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) sample_values = [] @@ -379,8 +378,10 @@ details=details, edit_mode=edit_mode) def __select_request_type(self, trans, rtid): + requesttype_list = trans.sa_session.query( trans.app.model.RequestType )\ + .order_by( trans.app.model.RequestType.name.asc() ) rt_ids = ['none'] - for rt in trans.sa_session.query( trans.app.model.RequestType ): + for rt in requesttype_list: if not rt.deleted: rt_ids.append(str(rt.id)) select_reqtype = SelectField('select_request_type', @@ -390,7 +391,7 @@ select_reqtype.add_option('Select one', 'none', selected=True) else: select_reqtype.add_option('Select one', 'none') - for rt in trans.sa_session.query( trans.app.model.RequestType ): + for rt in requesttype_list: if not rt.deleted: if rtid == rt.id: select_reqtype.add_option(rt.name, rt.id, selected=True) diff -r 5b2d593d9aed -r 0e78d558fe57 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Wed Nov 04 10:04:51 2009 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Wed Nov 04 10:16:20 2009 -0500 @@ -266,8 +266,10 @@ #---- Request Creation ---------------------------------------------------------- # def __select_request_type(self, trans, rtid): + requesttype_list = trans.sa_session.query( trans.app.model.RequestType )\ + .order_by( trans.app.model.RequestType.name.asc() ) rt_ids = ['none'] - for rt in trans.sa_session.query( trans.app.model.RequestType ): + for rt in requesttype_list: if not rt.deleted: rt_ids.append(str(rt.id)) select_reqtype = SelectField('select_request_type', @@ -277,7 +279,7 @@ select_reqtype.add_option('Select one', 'none', selected=True) else: select_reqtype.add_option('Select one', 'none') - for rt in trans.sa_session.query( trans.app.model.RequestType ): + for rt in requesttype_list: if not rt.deleted: if rtid == rt.id: select_reqtype.add_option(rt.name, rt.id, selected=True) @@ -799,7 +801,7 @@ # save all the new/unsaved samples entered by the user if edit_mode == 'False': for index in range(len(current_samples)-len(request.samples)): - sample_index = index + len(request.samples) + sample_index = len(request.samples) sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) sample_values = [] for field_index in range(len(request.type.sample_form.fields)): @@ -992,7 +994,7 @@ bar_code = util.restore_text(params.get('sample_%i_bar_code' % index, '')) # check for empty bar code if not bar_code.strip(): - msg = 'Please fill the bar code for sample <b>%s</b>.' % request.samples[index].name + msg = 'Please fill the barcode for sample <b>%s</b>.' % request.samples[index].name break # check all the unsaved bar codes count = 0 @@ -1000,8 +1002,8 @@ if bar_code == util.restore_text(params.get('sample_%i_bar_code' % i, '')): count = count + 1 if count > 1: - msg = '''The bar code <b>%s</b> of sample <b>%s</b> already belongs - another sample in this request. The sample bar codes must + msg = '''The barcode <b>%s</b> of sample <b>%s</b> belongs + another sample in this request. The sample barcodes must be unique throughout the system''' % \ (bar_code, request.samples[index].name) break @@ -1009,7 +1011,7 @@ all_samples = trans.sa_session.query( trans.app.model.Sample ) for sample in all_samples: if bar_code == sample.bar_code: - msg = '''The bar code <b>%s</b> of sample <b>%s</b> already + msg = '''The bar code <b>%s</b> of sample <b>%s</b> belongs another sample. The sample bar codes must be unique throughout the system''' % \ (bar_code, request.samples[index].name) @@ -1044,7 +1046,7 @@ return trans.response.send_redirect( web.url_for( controller='requests_admin', action='bar_codes', request_id=request.id, - msg='Bar codes has been saved for this request', + msg='Bar codes have been saved for this request', messagetype='done')) def __set_request_state(self, request): @@ -1162,8 +1164,8 @@ if params.get( 'create', False ): return trans.fill_template( '/admin/requests/create_request_type.mako', request_forms=get_all_forms( trans, - filter=dict(deleted=False), - form_type=trans.app.model.FormDefinition.types.REQUEST ), + filter=dict(deleted=False), + form_type=trans.app.model.FormDefinition.types.REQUEST ), sample_forms=get_all_forms( trans, filter=dict(deleted=False), form_type=trans.app.model.FormDefinition.types.SAMPLE ), diff -r 5b2d593d9aed -r 0e78d558fe57 templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Wed Nov 04 10:04:51 2009 -0500 +++ b/templates/admin/requests/show_request.mako Wed Nov 04 10:16:20 2009 -0500 @@ -195,7 +195,7 @@ <div class="toolForm"> ##<div class="toolFormTitle">Samples (${len(request.samples)})</div> - <form id="edit_form" name="edit_form" action="${h.url_for( controller='requests_admin', action='show_request' )}" enctype="multipart/form-data" method="post" > + <form id="show_request" name="show_request" action="${h.url_for( controller='requests_admin', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" > <div class="form-row"> %if current_samples: %if not request.type.sample_form.layout: diff -r 5b2d593d9aed -r 0e78d558fe57 templates/requests/show_request.mako --- a/templates/requests/show_request.mako Wed Nov 04 10:04:51 2009 -0500 +++ b/templates/requests/show_request.mako Wed Nov 04 10:16:20 2009 -0500 @@ -224,20 +224,16 @@ %endif </td> <td> - ##<div class="form-row"> <label>Import from csv file</label> <input type="file" name="file_data" /> <input type="submit" name="import_samples_button" value="Import samples"/> - ##</div> </td> <td> - ##<div class="form-row"> %if current_samples: <label>Copy from sample</label> ${sample_copy.get_html()} %endif <input type="submit" name="add_sample_button" value="Add New"/> - ##</div> </td> </div> </tr> diff -r 5b2d593d9aed -r 0e78d558fe57 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Nov 04 10:04:51 2009 -0500 +++ b/test/base/twilltestcase.py Wed Nov 04 10:16:20 2009 -0500 @@ -1272,7 +1272,7 @@ for index, bar_code in enumerate(bar_codes): tc.fv( "1", "sample_%i_bar_code" % index, bar_code ) tc.submit( "save_bar_codes" ) - self.check_page_for_string( 'Bar codes has been saved for this request' ) + self.check_page_for_string( 'Bar codes have been saved for this request' ) def change_sample_state( self, sample_name, sample_id, new_state_id, new_state_name, comment='' ): self.home() self.visit_url( "%s/requests_admin/show_events?sample_id=%i" % (self.url, sample_id) )

1 0

[hg] galaxy 2959: Fix tool test specification by id
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4bca8f8ed94d changeset: 2959:4bca8f8ed94d user: James Taylor <james(a)jamestaylor.org> date: Wed Nov 04 11:35:50 2009 -0500 description: Fix tool test specification by id diffstat: test/functional/test_toolbox.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (9 lines): diff -r 0e78d558fe57 -r 4bca8f8ed94d test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Wed Nov 04 10:16:20 2009 -0500 +++ b/test/functional/test_toolbox.py Wed Nov 04 11:35:50 2009 -0500 @@ -128,4 +128,4 @@ for j, testdef in enumerate( tool.tests ): name = "%s ( %s ) > %s" % ( tool.name, tool.id, testdef.name ) testcase = get_case( testdef, name ) - G[ 'testcase_%d_%d' % ( i, j ) ] = testcase + G[ testcase.__name__ ] = testcase

1 0

[hg] galaxy 2951: merge heads
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2300a80d80e5 changeset: 2951:2300a80d80e5 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Nov 03 13:04:35 2009 -0500 description: merge heads diffstat: lib/galaxy/tags/tag_handler.py | 8 +- lib/galaxy/web/controllers/history.py | 145 +++++++++++++++--- lib/galaxy/web/framework/helpers/grids.py | 1 + static/scripts/autocomplete_tagging.js | 2 +- static/scripts/packed/autocomplete_tagging.js | 2 +- static/scripts/packed/trackster.js | 2 +- templates/history/grid.mako | 250 +++++++++++++++++------------- test/base/twilltestcase.py | 18 +- test/functional/test_history_functions.py | 2 +- 9 files changed, 280 insertions(+), 150 deletions(-) diffs (665 lines): diff -r d872c1e16afb -r 2300a80d80e5 lib/galaxy/tags/tag_handler.py --- a/lib/galaxy/tags/tag_handler.py Tue Nov 03 12:52:01 2009 -0500 +++ b/lib/galaxy/tags/tag_handler.py Tue Nov 03 13:04:35 2009 -0500 @@ -3,6 +3,12 @@ class TagHandler( object ): + # Minimum tag length. + min_tag_len = 2 + + # Maximum tag length. + max_tag_len = 255 + # Tag separator. tag_separators = ',;' @@ -215,7 +221,7 @@ scrubbed_name = scrubbed_name[1:] # If name is too short or too long, return None. - if len(scrubbed_name) < 3 or len(scrubbed_name) > 255: + if len(scrubbed_name) < self.min_tag_len or len(scrubbed_name) > self.max_tag_len: return None return scrubbed_name diff -r d872c1e16afb -r 2300a80d80e5 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Tue Nov 03 12:52:01 2009 -0500 +++ b/lib/galaxy/web/controllers/history.py Tue Nov 03 13:04:35 2009 -0500 @@ -5,6 +5,7 @@ from galaxy.model import History from galaxy.model.orm import * from galaxy.util.json import * +from galaxy.util.odict import odict from galaxy.tags.tag_handler import TagHandler from sqlalchemy.sql.expression import ClauseElement import webhelpers, logging, operator @@ -19,12 +20,29 @@ class HistoryListGrid( grids.Grid ): # Custom column types class NameColumn( grids.GridColumn ): - def __init( self, key, link, attach_popup ): + def __init( self, key, link, attach_popup, filterable ): grids.GridColumn.__init__(self, key, link, attach_popup) def get_value( self, trans, grid, history ): return history.get_display_name() + def filter( self, db_session, query, column_filter ): + """ Modify query to filter histories by name. """ + if column_filter == "All": + pass + elif column_filter: + query = query.filter( func.lower( History.name ).like( "%" + column_filter.lower() + "%" ) ) + return query + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["FREETEXT"] = "FREETEXT" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.iteritems(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters + class DatasetsByStateColumn( grids.GridColumn ): def get_value( self, trans, grid, history ): rval = [] @@ -48,6 +66,7 @@ if item.users_shared_with or item.importable: return dict( operation="sharing" ) return None + class TagsColumn( grids.GridColumn ): def __init__( self, col_name, key, filterable ): grids.GridColumn.__init__(self, col_name, key=key, filterable=filterable) @@ -61,7 +80,7 @@ return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=history, elt_id = elt_id, in_form="true", input_size="20", tag_click_fn="add_tag_to_grid_filter" ) def filter( self, db_session, query, column_filter ): - """ Modify query to include only histories with tags in column_filter. """ + """ Modify query to filter histories by tag. """ if column_filter == "All": pass elif column_filter: @@ -69,52 +88,115 @@ tag_handler = TagHandler() raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) for name, value in raw_tags.items(): - tag = tag_handler.get_tag_by_name( db_session, name ) - if tag: - query = query.filter( History.tags.any( tag_id=tag.id ) ) + if name: + # Search for tag names. + query = query.filter( History.tags.any( func.lower( model.HistoryTagAssociation.user_tname ).like( "%" + name.lower() + "%" ) ) ) if value: - query = query.filter( History.tags.any( value=value.lower() ) ) - else: - # Tag doesn't exist; unclear what to do here, but the literal thing to do is add the criterion, which - # will then yield a query that returns no results. - query = query.filter( History.tags.any( user_tname=name ) ) + # Search for tag values. + query = query.filter( History.tags.any( func.lower( model.HistoryTagAssociation.user_value ).like( "%" + value.lower() + "%" ) ) ) return query def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = { "All": "All" } - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.items(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters - - + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["FREETEXT"] = "FREETEXT" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.iteritems(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters + class DeletedColumn( grids.GridColumn ): def get_accepted_filters( self ): """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = { "Active" : "False", "Deleted" : "True", "All": "All" } + accepted_filter_labels_and_vals = { "active" : "False", "deleted" : "True", "all": "All" } accepted_filters = [] for label, val in accepted_filter_labels_and_vals.items(): args = { self.key: val } accepted_filters.append( grids.GridColumnFilter( label, args) ) return accepted_filters + + class SharingColumn( grids.GridColumn ): + def filter( self, db_session, query, column_filter ): + """ Modify query to filter histories by sharing status. """ + if column_filter == "All": + pass + elif column_filter: + if column_filter == "private": + query = query.filter( History.users_shared_with == None ) + query = query.filter( History.importable == False ) + elif column_filter == "shared": + query = query.filter( History.users_shared_with != None ) + elif column_filter == "importable": + query = query.filter( History.importable == True ) + return query + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["private"] = "private" + accepted_filter_labels_and_vals["shared"] = "shared" + accepted_filter_labels_and_vals["importable"] = "importable" + accepted_filter_labels_and_vals["all"] = "All" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.items(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters + + class FreeTextSearchColumn( grids.GridColumn ): + def filter( self, db_session, query, column_filter ): + """ Modify query to search tags and history names. """ + if column_filter == "All": + pass + elif column_filter: + # Build tags filter. + tag_handler = TagHandler() + raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) + tags_filter = None + for name, value in raw_tags.items(): + if name: + # Search for tag names. + tags_filter = History.tags.any( func.lower( model.HistoryTagAssociation.user_tname ).like( "%" + name.lower() + "%" ) ) + if value: + # Search for tag values. + tags_filter = and_( tags_filter, func.lower( History.tags.any( model.HistoryTagAssociation.user_value ).like( "%" + value.lower() + "%" ) ) ) + + # Build history name filter. + history_name_filter = func.lower( History.name ).like( "%" + column_filter.lower() + "%" ) + + # Apply filters to query. + if tags_filter: + query = query.filter( or_( tags_filter, history_name_filter ) ) + else: + query = query.filter( history_name_filter ) + return query + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["FREETEXT"] = "FREETEXT" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.iteritems(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters # Grid definition - title = "Stored histories" + title = "Saved Histories" model_class = model.History template='/history/grid.mako' default_sort_key = "-create_time" columns = [ NameColumn( "Name", key="name", link=( lambda history: iff( history.deleted, None, dict( operation="switch", id=history.id ) ) ), - attach_popup=True ), + attach_popup=True, filterable=True ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), TagsColumn( "Tags", key="tags", filterable=True), StatusColumn( "Status", attach_popup=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), - # Valid for filtering but invisible - DeletedColumn( "Status", key="deleted", visible=False, filterable=True ) + # Columns that are valid for filtering but are not visible. + DeletedColumn( "Deleted", key="deleted", visible=False, filterable=True ), + SharingColumn( "Shared", key="shared", visible=False, filterable=True ), + FreeTextSearchColumn( "Search", key="free-text-search", visible=False ) # Not filterable because it's the default search. ] operations = [ grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ) ), @@ -131,7 +213,7 @@ grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), grids.GridColumnFilter( "All", args=dict( deleted='All' ) ), ] - default_filter = dict( deleted="False", tags="All" ) + default_filter = dict( name="All", deleted="False", tags="All", shared="All" ) num_rows_per_page = 50 preserve_state = False use_paging = True @@ -160,6 +242,7 @@ template='/history/grid.mako' model_class = model.History default_sort_key = "-update_time" + default_filter = {} columns = [ grids.GridColumn( "Name", key="name" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), @@ -374,6 +457,18 @@ trans.sa_session.flush() @web.expose + def name_autocomplete_data( self, trans, q=None, limit=None, timestamp=None ): + """Return autocomplete data for history names""" + user = trans.get_user() + if not user: + return + + ac_data = "" + for history in trans.sa_session.query( History ).filter_by( user=user ).filter( func.lower( History.name ) .like(q.lower() + "%") ): + ac_data = ac_data + history.name + "\n" + return ac_data + + @web.expose def imp( self, trans, id=None, confirm=False, **kwd ): """Import another user's history via a shared URL""" msg = "" diff -r d872c1e16afb -r 2300a80d80e5 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Tue Nov 03 12:52:01 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Tue Nov 03 13:04:35 2009 -0500 @@ -183,6 +183,7 @@ query=query, cur_page_num = page_num, num_pages = num_pages, + default_filter_dict=self.default_filter, cur_filter_dict=cur_filter_dict, sort_key=sort_key, encoded_sort_key=encoded_sort_key, diff -r d872c1e16afb -r 2300a80d80e5 static/scripts/autocomplete_tagging.js --- a/static/scripts/autocomplete_tagging.js Tue Nov 03 12:52:01 2009 -0500 +++ b/static/scripts/autocomplete_tagging.js Tue Nov 03 13:04:35 2009 -0500 @@ -309,7 +309,7 @@ new_value = new_value.replace(/^\s+|\s+$/g,""); // Too short? - if (new_value.length < 3) + if (new_value.length < 2) return false; // diff -r d872c1e16afb -r 2300a80d80e5 static/scripts/packed/autocomplete_tagging.js --- a/static/scripts/packed/autocomplete_tagging.js Tue Nov 03 12:52:01 2009 -0500 +++ b/static/scripts/packed/autocomplete_tagging.js Tue Nov 03 13:04:35 2009 -0500 @@ -1,1 +1,1 @@ -var ac_tag_area_id_gen=1;jQuery.fn.autocomplete_tagging=function(c){var e={get_toggle_link_text_fn:function(u){var w="";var v=o(u);if(v!=0){w=v+(v!=0?" Tags":" Tag")}else{w="Add tags"}return w},tag_click_fn:function(u,v){},editable:true,input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var p=jQuery.extend(e,c);var k="tag-area-"+(ac_tag_area_id_gen)++;var m=$("<div>").attr("id",k).addClass("tag-area");this.append(m);var o=function(u){if(u.length){return u.length}var v=0;for(element in u){v++}return v};var b=function(){var u=p.get_toggle_link_text_fn(p.tags);var v=$("<a href='/history/tags'>").text(u).addClass("toggle-link");v.click(function(){var w=(m.css("display")=="none");var x;if(w){x=function(){var y=o(p.tags);if(y==0){m.click()}}}else{x=function(){m.blur()}}m.slideToggle("fast",x);return false});return v};v ar s=b();if(p.use_toggle_link){this.prepend(s)}var t=function(u){var v=new Array();for(key in u){v[v.length]=key+"-->"+u[key]}return"{"+v.join(",")+"}"};var a=function(v,u){return v+((u!=""&&u)?":"+u:"")};var h=function(u){return u.split(":")};var i=function(u){var v=$("<img src='"+p.add_tag_img+"' rollover='"+p.add_tag_img_rollover+"'/>").addClass("add-tag-button");v.click(function(){$(this).hide();m.click();return false});return v};var j=function(u){var v=$("<img src='"+p.delete_tag_img+"'/>").addClass("delete-tag-img");v.mouseenter(function(){$(this).attr("src",p.delete_tag_img_rollover)});v.mouseleave(function(){$(this).attr("src",p.delete_tag_img)});v.click(function(){var D=$(this).parent();var C=D.find(".tag-name").eq(0);var B=C.text();var z=h(B);var F=z[0];var y=z[1];var E=D.prev();D.remove();delete p.tags[F];var A=p.get_toggle_link_text_fn(p.tags);s.text(A);$.ajax({url:p.ajax_delete_tag_url,data:{tag_name:F},error:function(){p.tags[F]=y;if(E.hasClass("tag-button")){E .after(D)}else{m.prepend(D)}var G=p.get_toggle_link_text_fn(p.tags);alert("Remove tag failed");s.text(G);v.mouseenter(function(){$(this).attr("src",p.delete_tag_img_rollover)});v.mouseleave(function(){$(this).attr("src",p.delete_tag_img)})},success:function(){}});return true});var w=$("<span>").text(u).addClass("tag-name");w.click(function(){tag_name_and_value=u.split(":");p.tag_click_fn(tag_name_and_value[0],tag_name_and_value[1]);return true});var x=$("<span></span>").addClass("tag-button");x.append(w);if(p.editable){x.append(v)}return x};var d=function(v){var u;if(p.in_form){u=$("<textarea id='history-tag-input' rows='1' cols='"+p.input_size+"' value='"+escape(v)+"'></textarea>")}else{u=$("<input id='history-tag-input' type='text' size='"+p.input_size+"' value='"+escape(v)+"'></input>")}u.keyup(function(D){if(D.keyCode==27){$(this).trigger("blur")}else{if((D.keyCode==13)||(D.keyCode==188)||(D.keyCode==32)){new_value=this.value;if(return_key_pressed_for_autocomplete==true) {return_key_pressed_for_autocomplete=false;return false}if(new_value.indexOf(": ",new_value.length-2)!=-1){this.value=new_value.substring(0,new_value.length-1);return false}if((D.keyCode==188)||(D.keyCode==32)){new_value=new_value.substring(0,new_value.length-1)}new_value=new_value.replace(/^\s+|\s+$/g,"");if(new_value.length<3){return false}this.value="";var A=j(new_value);var z=m.children(".tag-button");if(z.length!=0){var E=z.slice(z.length-1);E.after(A)}else{m.prepend(A)}var y=new_value.split(":");p.tags[y[0]]=y[1];var B=p.get_toggle_link_text_fn(p.tags);s.text(B);var C=$(this);$.ajax({url:p.ajax_add_tag_url,data:{new_tag:new_value},error:function(){A.remove();delete p.tags[y[0]];var F=p.get_toggle_link_text_fn(p.tags);s.text(F);alert("Add tag failed")},success:function(){C.flushCache()}});return false}}});var w=function(A,z,y,C,B){tag_name_and_value=C.split(":");return(tag_name_and_value.length==1?tag_name_and_value[0]:tag_name_and_value[1])};var x={selectFirst:false,fo rmatItem:w,autoFill:false,highlight:false};u.autocomplete(p.ajax_autocomplete_tag_url,x);u.addClass("tag-input");return u};for(tag_name in p.tags){var q=p.tags[tag_name];var l=a(tag_name,q);var g=j(l,s,p.tags);m.append(g)}var n=d("");var f=i(n);m.blur(function(u){r=o(p.tags);if(r!=0){f.show();n.hide();m.removeClass("active-tag-area")}else{}});if(p.editable){m.append(f);m.append(n);n.hide();m.click(function(w){var v=$(this).hasClass("active-tag-area");if($(w.target).hasClass("delete-tag-img")&&!v){return false}if($(w.target).hasClass("tag-name")&&!v){return false}$(this).addClass("active-tag-area");f.hide();n.show();n.focus();var u=function(y){var x=m.attr("id");if(($(y.target).attr("id")!=x)&&($(y.target).parents().filter(x).length==0)){m.blur();$(document).unbind("click",u)}};$(window).click(u);return false})}if(p.use_toggle_link){m.hide()}else{var r=o(p.tags);if(r==0){f.hide();n.show()}}return this.addClass("tag-element")}; \ No newline at end of file +var ac_tag_area_id_gen=1;jQuery.fn.autocomplete_tagging=function(c){var e={get_toggle_link_text_fn:function(u){var w="";var v=o(u);if(v!=0){w=v+(v!=0?" Tags":" Tag")}else{w="Add tags"}return w},tag_click_fn:function(u,v){},editable:true,input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var p=jQuery.extend(e,c);var k="tag-area-"+(ac_tag_area_id_gen)++;var m=$("<div>").attr("id",k).addClass("tag-area");this.append(m);var o=function(u){if(u.length){return u.length}var v=0;for(element in u){v++}return v};var b=function(){var u=p.get_toggle_link_text_fn(p.tags);var v=$("<a href='/history/tags'>").text(u).addClass("toggle-link");v.click(function(){var w=(m.css("display")=="none");var x;if(w){x=function(){var y=o(p.tags);if(y==0){m.click()}}}else{x=function(){m.blur()}}m.slideToggle("fast",x);return false});return v};v ar s=b();if(p.use_toggle_link){this.prepend(s)}var t=function(u){var v=new Array();for(key in u){v[v.length]=key+"-->"+u[key]}return"{"+v.join(",")+"}"};var 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",new_value.length-2)!=-1){this.value=new_value.substring(0,new_value.length-1);return false}if((D.keyCode==188)||(D.keyCode==32)){new_value=new_value.substring(0,new_value.length-1)}new_value=new_value.replace(/^\s+|\s+$/g,"");if(new_value.length<2){return false}this.value="";var A=j(new_value);var z=m.children(".tag-button");if(z.length!=0){var E=z.slice(z.length-1);E.after(A)}else{m.prepend(A)}var y=new_value.split(":");p.tags[y[0]]=y[1];var B=p.get_toggle_link_text_fn(p.tags);s.text(B);var C=$(this);$.ajax({url:p.ajax_add_tag_url,data:{new_tag:new_value},error:function(){A.remove();delete p.tags[y[0]];var F=p.get_toggle_link_text_fn(p.tags);s.text(F);alert("Add tag failed")},success:function(){C.flushCache()}});return false}}});var w=function(A,z,y,C,B){tag_name_and_value=C.split(":");return(tag_name_and_value.length==1?tag_name_and_value[0]:tag_name_and_value[1])};var x={selectFirst:false,fo rmatItem:w,autoFill:false,highlight:false};u.autocomplete(p.ajax_autocomplete_tag_url,x);u.addClass("tag-input");return u};for(tag_name in p.tags){var q=p.tags[tag_name];var l=a(tag_name,q);var g=j(l,s,p.tags);m.append(g)}var n=d("");var f=i(n);m.blur(function(u){r=o(p.tags);if(r!=0){f.show();n.hide();m.removeClass("active-tag-area")}else{}});if(p.editable){m.append(f);m.append(n);n.hide();m.click(function(w){var v=$(this).hasClass("active-tag-area");if($(w.target).hasClass("delete-tag-img")&&!v){return false}if($(w.target).hasClass("tag-name")&&!v){return false}$(this).addClass("active-tag-area");f.hide();n.show();n.focus();var u=function(y){var x=m.attr("id");if(($(y.target).attr("id")!=x)&&($(y.target).parents().filter(x).length==0)){m.blur();$(document).unbind("click",u)}};$(window).click(u);return false})}if(p.use_toggle_link){m.hide()}else{var r=o(p.tags);if(r==0){f.hide();n.show()}}return this.addClass("tag-element")}; \ No newline at end of file diff -r d872c1e16afb -r 2300a80d80e5 static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Tue Nov 03 12:52:01 2009 -0500 +++ b/static/scripts/packed/trackster.js Tue Nov 03 13:04:35 2009 -0500 @@ -1,1 +1,1 @@ -var DENSITY=1000,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES=5,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(l eft_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var 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c=Math.pow(10,Math.ceil(Math.log(e/DENSITY)/Math.log(10)));c=Math.max(c,0.1);c=Math.min(c,1000000);var j=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(j);var k=this.content_div.width()/e;var g;var a=Math.floor(h/c/DENSITY);while((a*DENSITY*c)<d){var i=this.view.zoom_level+"_"+a;var b=this.tile_cache.get(i);if(b){var f=a*DENSITY*c;b.css({left:(f-this.view.low)*k});j.append(b)}else{g=this.draw_tile(c,a,j,k)}if(g){this.tile_cache.set(i,g)}a+=1}}});var LabelTrack=function(a){Track.ca ll(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.dataset_id=b;this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dat aset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_px+32+"px",});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id},function(g){c.cache[e]=g;$(document).trigger("redra w")})},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache[l]){this.get_data(d,a);return}var g=this.cache[l];c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);return c}});var FeatureTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143"};$.extend(FeatureTrack.prototype,TiledTrack.pro totype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},calc_slots:function(o){var c=[],b=this.container_div.width()/(this.view.high-this.view.low),g=this.show_labels_scale,a=this.view.max_high,e=this.view.max_low;if(o){this.zi_slots={}}var m=$("<canvas></canvas>").get(0).getContext("2d");for(var f=0,h=this.values.length;f<h;f++){var k,l,n=this.values[f];if(o){k=Math.floor(Math.max(e,(n.star t-e)*g));k-=m.measureText(n.name).width;l=Math.ceil(Math.min(a,(n.end-e)*g))}else{k=Math.floor(Math.max(e,(n.start-e)*b));l=Math.ceil(Math.min(a,(n.end-e)*b))}var d=0;while(true){if(c[d]===undefined||c[d]<k){c[d]=l;if(o){this.zi_slots[n.name]=d}else{this.zo_slots[n.name]=d}break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},draw_tile:function(w,B,g,n){if(!this.values){return null}if(n>this.show_labels_scale&&!this.showing_labels){this.showing_labels=true;if(!this.zi_slots){this.calc_slots(true)}this.slots=this.zi_slots}else{if(n<=this.show_labels_scale&&this.showing_labels){this.showing_labels=false;this.slots=this.zo_slots}}var C=B*DENSITY*w,c=(B+1)*DENSITY*w,q=DENSITY*w;var u=Math.ceil(q*n),t=this.height_px,s=$("<canvas class='tile'></canvas>");s.css({position:"absolute",top:0,left:(C-this.view.low)*n});s.get(0).width=u;s.get(0).height=t;var v=s.get(0).getContext("2d");v.fillStyle=this.base_color;v.font="10px monospac e";v.textAlign="right";var y=0;for(var z=0,A=this.values.length;z<A;z++){var f=this.values[z];if(f.start<=c&&f.end>=C){var e=Math.floor(Math.max(0,(f.start-C)*n)),h=Math.ceil(Math.min(u,(f.end-C)*n)),d=this.slots[f.name]*this.vertical_gap;var a,G,b=null,o=null;if(f.thick_start&&f.thick_end){b=Math.floor(Math.max(0,(f.thick_start-C)*n));o=Math.ceil(Math.min(u,(f.thick_end-C)*n))}if(!this.showing_labels){v.fillRect(e,d+5,h-e,1)}else{if(v.fillText){v.fillText(f.name,e-1,d+8)}var E=f.blocks;if(E){if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND}else{if(f.strand=="-"){v.fillStyle=LEFT_STRAND}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}for(var x=0,F=E.length;x<F;x++){var m=E[x],l=Math.floor(Math.max(0,(m[0]-C)*n)),D=Math.ceil(Math.min(u,(m[1]-C)*n));a=5;G=3;v.fillRect(l,d+G,D-l,a);if(b&&(l<o||D>b)){a=9;G=1;var r=Math.max(l,b),p=Math.min(D,o);v.fillRect(r,d+G,p-r,a)}}}else{a=9;G=1;v.fillRect(e,d+G,h-e,a);if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND_INV}els e{if(f.strand=="-"){v.fillStyle=LEFT_STRAND_INV}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}}}y++}}g.append(s);return s}}); \ No newline at end of file +var DENSITY=1000,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES=10,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern( left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=2;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){ e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}$("#bottom-spacer").remove();$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>')},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){th is.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){this.tile_cache=new Cache(CACHED_TILES)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var h=this.view.low,d=this.view.high,e=d-h;var c=Math.pow(10,Math.ceil(Math.log(e/DENSITY)/Math.log(10)));c=Math.max(c,0.1);c=Math.min(c,1000000);var j=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(j);var k=this.content_div.width()/e;var g;var a=Math.floor(h/c/DENSITY);while((a*DENSITY*c)<d){var i=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var b=this.tile_cache.get(i);if(b){var f=a*DENSITY*c;b.css({left:(f-this.view.low)*k});j.append(b)}else{g=this.draw_tile(c,a,j,k);if(g){this.tile_cache.set(i,g)}}a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.dataset_id=b;this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low: null,high:null,dataset_id:a.dataset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_px+32+"px",});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id},function(g){c.cache[ e]=g;$(document).trigger("redraw")})},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache[l]){this.get_data(d,a);return}var g=this.cache[l];c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);return c}});var FeatureTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143"};$.extend(Featur eTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},calc_slots:function(o){var c=[],b=this.content_div.width()/(this.view.high-this.view.low),g=this.show_labels_scale,a=this.view.max_high,e=this.view.max_low;if(o){this.zi_slots={}}var m=$("<canvas></canvas>").get(0).getContext("2d");for(var f=0,h=this.values.length;f<h;f++){var k,l,n=this.values[f];if(o){k= Math.floor((n.start-e)*g);k-=m.measureText(n.name).width;l=Math.ceil((n.end-e)*g)}else{k=Math.floor((n.start-e)*b);l=Math.ceil((n.end-e)*b)}var d=0;while(true){if(c[d]===undefined||c[d]<k){c[d]=l;if(o){this.zi_slots[n.name]=d}else{this.zo_slots[n.name]=d}break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},draw_tile:function(w,B,g,n){if(!this.values){return null}if(n>this.show_labels_scale&&!this.showing_labels){this.showing_labels=true;if(!this.zi_slots){this.calc_slots(true)}this.slots=this.zi_slots}else{if(n<=this.show_labels_scale&&this.showing_labels){this.showing_labels=false;this.slots=this.zo_slots}}var C=B*DENSITY*w,c=(B+1)*DENSITY*w,q=DENSITY*w;var u=Math.ceil(q*n),t=this.height_px,s=$("<canvas class='tile'></canvas>");s.css({position:"absolute",top:0,left:(C-this.view.low)*n});s.get(0).width=u;s.get(0).height=t;var v=s.get(0).getContext("2d");v.fillStyle=this.base_color;v.font="10px monospace";v.textAlign="rig ht";var y=0;for(var z=0,A=this.values.length;z<A;z++){var f=this.values[z];if(f.start<=c&&f.end>=C){var e=Math.floor(Math.max(0,(f.start-C)*n)),h=Math.ceil(Math.min(u,(f.end-C)*n)),d=this.slots[f.name]*this.vertical_gap;var a,G,b=null,o=null;if(f.thick_start&&f.thick_end){b=Math.floor(Math.max(0,(f.thick_start-C)*n));o=Math.ceil(Math.min(u,(f.thick_end-C)*n))}if(!this.showing_labels){v.fillRect(e,d+5,h-e,1)}else{if(v.fillText){v.fillText(f.name,e-1,d+8)}var E=f.blocks;if(E){if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND}else{if(f.strand=="-"){v.fillStyle=LEFT_STRAND}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}for(var x=0,F=E.length;x<F;x++){var m=E[x],l=Math.floor(Math.max(0,(m[0]-C)*n)),D=Math.ceil(Math.min(u,(m[1]-C)*n));a=5;G=3;v.fillRect(l,d+G,D-l,a);if(b&&(l<o||D>b)){a=9;G=1;var r=Math.max(l,b),p=Math.min(D,o);v.fillRect(r,d+G,p-r,a)}}}else{a=9;G=1;v.fillRect(e,d+G,h-e,a);if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND_INV}else{if(f.strand=="-") {v.fillStyle=LEFT_STRAND_INV}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}}}y++}}g.append(s);return s}}); \ No newline at end of file diff -r d872c1e16afb -r 2300a80d80e5 templates/history/grid.mako --- a/templates/history/grid.mako Tue Nov 03 12:52:01 2009 -0500 +++ b/templates/history/grid.mako Tue Nov 03 13:04:35 2009 -0500 @@ -29,71 +29,20 @@ }); // Set up autocomplete for tag filter input. - var t = $("#input-tag-filter"); - t.keyup( function( e ) - { - if ( e.keyCode == 27 ) - { - // Escape key - $(this).trigger( "blur" ); - } else if ( - ( e.keyCode == 13 ) || // Return Key - ( e.keyCode == 188 ) || // Comma - ( e.keyCode == 32 ) // Space - ) - { - // - // Check input. - // - - new_value = this.value; - - // Do nothing if return key was used to autocomplete. - if (return_key_pressed_for_autocomplete == true) - { - return_key_pressed_for_autocomplete = false; - return false; - } - - // Suppress space after a ":" - if ( new_value.indexOf(": ", new_value.length - 2) != -1) - { - this.value = new_value.substring(0, new_value.length-1); - return false; - } - - // Remove trigger keys from input. - if ( (e.keyCode == 188) || (e.keyCode == 32) ) - new_value = new_value.substring( 0 , new_value.length - 1 ); - - // Trim whitespace. - new_value = new_value.replace(/^\s+|\s+$/g,""); - - // Too short? - if (new_value.length < 3) - return false; - - // - // New tag OK. - // - } - }); + var t = $("#input-tags-filter"); - // Add autocomplete to input. - var format_item_func = function(key, row_position, num_rows, value, search_term) - { - tag_name_and_value = value.split(":"); - return (tag_name_and_value.length == 1 ? tag_name_and_value[0] :tag_name_and_value[1]); - //var array = new Array(key, value, row_position, num_rows, - //search_term ); return "\"" + array.join("*") + "\""; - } var autocomplete_options = - { selectFirst: false, formatItem : format_item_func, autoFill: false, highlight: false, mustMatch: true }; + { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; t.autocomplete("${h.url_for( controller='tag', action='tag_autocomplete_data', item_class='History' )}", autocomplete_options); - - $("#page-select").change(navigate_to_page); + // Set up autocomplete for name filter input. + var t2 = $("#input-name-filter"); + + var autocomplete_options = + { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; + + t2.autocomplete("${h.url_for( controller='history', action='name_autocomplete_data' )}", autocomplete_options); }); ## Can this be moved into base.mako? %if refresh_frames: @@ -125,21 +74,52 @@ %endif %endif + // Filter and sort args for grid. + var filter_args = ${h.to_json_string(cur_filter_dict)}; + var sort_key = "${sort_key}"; + // - // Add a tag to the current grid filter; this adds the tag to the filter and then issues a request to refresh the grid. + // Add tag to grid filter. // function add_tag_to_grid_filter(tag_name, tag_value) { - // Use tag as a filter: replace TAGNAME with tag_name and issue query. - <% - url_args = {} - if "tags" in cur_filter_dict and cur_filter_dict["tags"] != "All": - url_args["f-tags"] = cur_filter_dict["tags"].encode("utf-8") + ", TAGNAME" - else: - url_args["f-tags"] = "TAGNAME" - %> - var url_base = "${url( url_args )}"; - var url = url_base.replace("TAGNAME", tag_name); + // Put tag name and value together. + var tag = tag_name + (tag_value != null && tag_value != "" ? ":" + tag_value : ""); + add_condition_to_grid_filter("tags", tag, true); + } + + // + // Add a filter to the current grid filter; this adds the filter and then issues a request to refresh the grid. + // + function add_condition_to_grid_filter(name, value, append) + { + // Update filter arg with new condition. + if (append) + { + // Append value. + var cur_val = filter_args[name]; + if (cur_val != "All") + cur_val = cur_val + ", " + value; + else + cur_val = value; + filter_args[name] = cur_val; + } + else + { + // Replace value. + filter_args[name] = value; + } + + // Build URL with filter args, sort key. + var filter_arg_value_strs = new Array(); + var i = 0; + for (arg in filter_args) + { + filter_arg_value_strs[i++] = "f-" + arg + "=" + filter_args[arg]; + } + var filter_str = filter_arg_value_strs.join("&"); + var url_base = "${h.url_for( controller='history', action='list')}"; + var url = url_base + "?" + filter_str + "&sort=" + sort_key; self.location = url; } @@ -154,7 +134,7 @@ var url = url_base.replace("PAGE", page_num); self.location = url; } - + </script> </%def> @@ -175,47 +155,95 @@ <div class="grid-header"> <h2>${grid.title}</h2> - - ## Print grid filter. - <form name="history_actions" action="javascript:add_tag_to_grid_filter($('#input-tag-filter').attr('value'))" method="get" > - <strong>Filter:   </strong> - %for column in grid.columns: - %if column.filterable: - <span> by ${column.label.lower()}:</span> - ## For now, include special case to handle tags. - %if column.key == "tags": - %if cur_filter_dict[column.key] != "All": - <span class="filter" "style='font-style: italic'"> - ${cur_filter_dict[column.key]} - </span> - <span>|</span> + + ## Search box and more options filter at top of grid. + <div> + ## Grid search. TODO: use more elegant way to get free text search column. + <% column = grid.columns[-1] %> + <% use_form = False %> + %for i, filter in enumerate( column.get_accepted_filters() ): + %if i > 0: + <span>|</span> + %endif + %if column.key in cur_filter_dict and cur_filter_dict[column.key] == filter.args[column.key]: + <span class="filter" "style='font-style: italic'">${filter.label}</span> + %elif filter.label == "FREETEXT": + <form name="history_actions" + action="javascript:add_condition_to_grid_filter($('#input-${column.key}-filter').attr('name'),$('#input-${column.key}-filter').attr('value'),false)" + method="get" > + ${column.label}: + %if column.key in cur_filter_dict and cur_filter_dict[column.key] != "All": + <span style="font-style: italic">${cur_filter_dict[column.key]}</span> + <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> + <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + | %endif - <input id="input-tag-filter" name="f-tags" type="text" value="" size="15"/> - <span>|</span> - %endif - - ## Handle other columns. - %for i, filter in enumerate( column.get_accepted_filters() ): - %if i > 0: - <span>|</span> - %endif - %if cur_filter_dict[column.key] == filter.args[column.key]: - <span class="filter" "style='font-style: italic'">${filter.label}</span> - %else: - <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> - %endif - %endfor - <span>     </span> + <span><input id="input-${column.key}-filter" name="${column.key}" type="text" value="" size="15"/></span> + <% use_form = True %> + %else: + <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> %endif %endfor - - ## Link to clear all filters. TODO: this should be the default filter or an empty filter. - <% - args = { "deleted" : "False", "tags" : "All" } - no_filter = GridColumnFilter("Clear Filter", args) - %> - <span><a href="${url( no_filter.get_url_args() )}">${no_filter.label}</a></span> - </form> + | <a href="" onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Advanced Search</a> + %if use_form: + </form> + %endif + </div> + + ## Advanced Search + <div id="more-search-options" style="display: none; padding-top: 5px"> + <table style="border: 1px solid gray;"> + <tr><td style="text-align: left" colspan="100"> + Advanced Search | + <a href=""# onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Close</a> | + ## Link to clear all filters. + <% + no_filter = GridColumnFilter("Clear All", default_filter_dict) + %> + <a href="${url( no_filter.get_url_args() )}">${no_filter.label}</a> + </td></tr> + %for column in grid.columns: + %if column.filterable: + <tr> + ## Show div if current filter has value that is different from the default filter. + %if cur_filter_dict[column.key] != default_filter_dict[column.key]: + <script type="text/javascript"> + $('#more-search-options').css("display", "block"); + </script> + %endif + <td style="padding-left: 10px">${column.label.lower()}:</td> + <td> + <% use_form = False %> + %for i, filter in enumerate( column.get_accepted_filters() ): + %if i > 0: + <span>|</span> + %endif + %if cur_filter_dict[column.key] == filter.args[column.key]: + <span class="filter" style="font-style: italic">${filter.label}</span> + %elif filter.label == "FREETEXT": + <form name="history_actions" action="javascript:add_condition_to_grid_filter($('#input-${column.key}-filter').attr('name'),$('#input-${column.key}-filter').attr('value'),true)" + method="get" > + %if column.key in cur_filter_dict and cur_filter_dict[column.key] != "All": + <span style="font-style: italic">${cur_filter_dict[column.key]}</span> + <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> + <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + | + %endif + <span><input id="input-${column.key}-filter" name="${column.key}" type="text" value="" size="15"/></span> + <% use_form = True %> + %else: + <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> + %endif + %endfor + %if use_form: + </form> + %endif + </td> + </tr> + %endif + %endfor + </table> + </div> </div> <form name="history_actions" action="${url()}" method="post" > <input type="hidden" name="page" value="${cur_page_num}"> @@ -291,7 +319,7 @@ extra = "" %> %if href: - <td><div class="menubutton split" style="float: left;"><a class="label" href="${href}">${v}${extra}</a> </td> + <td><div class="menubutton split" style="float: left;"><a class="label" href="${href}">${v}</a>${extra}</td> %else: <td >${v}${extra}</td> %endif diff -r d872c1e16afb -r 2300a80d80e5 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Tue Nov 03 12:52:01 2009 -0500 +++ b/test/base/twilltestcase.py Tue Nov 03 13:04:35 2009 -0500 @@ -1,7 +1,7 @@ import pkg_resources pkg_resources.require( "twill==0.9" ) -import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, zipfile, tempfile +import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, zipfile, tempfile, re from itertools import * import twill @@ -311,20 +311,20 @@ def view_stored_active_histories( self, check_str='' ): self.home() self.visit_page( "history/list" ) - self.check_page_for_string( 'Stored histories' ) + self.check_page_for_string( 'Saved Histories' ) self.check_page_for_string( '<input type="checkbox" name="id" value=' ) - self.check_page_for_string( 'operation=Rename&id' ) - self.check_page_for_string( 'operation=Switch&id' ) - self.check_page_for_string( 'operation=Delete&id' ) + self.check_page_for_string( 'operation=Rename' ) + self.check_page_for_string( 'operation=Switch' ) + self.check_page_for_string( 'operation=Delete' ) if check_str: self.check_page_for_string( check_str ) self.home() def view_stored_deleted_histories( self, check_str='' ): self.home() self.visit_page( "history/list?f-deleted=True" ) - self.check_page_for_string( 'Stored histories' ) + self.check_page_for_string( 'Saved Histories' ) self.check_page_for_string( '<input type="checkbox" name="id" value=' ) - self.check_page_for_string( 'operation=Undelete&id' ) + self.check_page_for_string( 'operation=Undelete' ) if check_str: self.check_page_for_string( check_str ) self.home() @@ -723,14 +723,14 @@ # Functions associated with browsers, cookies, HTML forms and page visits def check_page_for_string( self, patt ): - """Looks for 'patt' in the current browser page""" + """Looks for 'patt' in the current browser page""" page = self.last_page() for subpatt in patt.split(): if page.find( patt ) == -1: fname = self.write_temp_file( page ) errmsg = "no match to '%s'\npage content written to '%s'" % ( patt, fname ) raise AssertionError( errmsg ) - + def write_temp_file( self, content ): fd, fname = tempfile.mkstemp( suffix='.html', prefix='twilltestcase-' ) f = os.fdopen( fd, "w" ) diff -r d872c1e16afb -r 2300a80d80e5 test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Tue Nov 03 12:52:01 2009 -0500 +++ b/test/functional/test_history_functions.py Tue Nov 03 13:04:35 2009 -0500 @@ -179,7 +179,7 @@ self.share_current_history( regular_user1.email, check_str=history3.name ) # Check out list of histories to make sure history3 was shared - self.view_stored_active_histories( check_str='operation=sharing">shared' ) + self.view_stored_active_histories( check_str='operation=sharing' ) # Enable importing history3 via a URL self.enable_import_via_link( self.security.encode_id( history3.id ), check_str='Unshare',

1 0

[hg] galaxy 2950: imported patch alchemy05_fixes_02
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d872c1e16afb changeset: 2950:d872c1e16afb user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Nov 03 12:52:01 2009 -0500 description: imported patch alchemy05_fixes_02 diffstat: lib/galaxy/jobs/__init__.py | 6 +++--- lib/galaxy/model/mapping.py | 4 ++-- lib/galaxy/model/mapping_tests.py | 15 ++++++++------- lib/galaxy/model/migrate/versions/0025_user_info.py | 4 ++-- lib/galaxy/tools/actions/__init__.py | 7 ++++--- lib/galaxy/tools/actions/metadata.py | 5 +++-- lib/galaxy/tools/actions/upload_common.py | 4 +++- lib/galaxy/web/controllers/async.py | 6 +++--- lib/galaxy/web/controllers/dataset.py | 4 ++-- lib/galaxy/web/controllers/library.py | 6 +++--- lib/galaxy/web/controllers/library_admin.py | 12 ++++++++---- lib/galaxy/web/controllers/requests.py | 2 +- lib/galaxy/web/controllers/root.py | 10 +++++----- lib/galaxy/web/controllers/tool_runner.py | 2 -- lib/galaxy/web/framework/__init__.py | 23 ++++++++++++++--------- test/functional/test_forms_and_requests.py | 1 + test/functional/test_security_and_libraries.py | 2 +- test/functional/test_user_info.py | 3 ++- tools/data_source/microbial_import_code.py | 6 +++--- tools/filters/lav_to_bed_code.py | 1 - tools/maf/maf_to_bed_code.py | 4 +--- 21 files changed, 69 insertions(+), 58 deletions(-) diffs (567 lines): diff -r 133252175425 -r d872c1e16afb lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/jobs/__init__.py Tue Nov 03 12:52:01 2009 -0500 @@ -199,7 +199,7 @@ try: # Clear the session for each job so we get fresh states for # job and all datasets - self.sa_session.clear() + self.sa_session.expunge_all() # Get the real job entity corresponding to the wrapper (if we # are tracking in the database this is probably cached in # the session from the origianl query above) @@ -346,7 +346,7 @@ Prepare the job to run by creating the working directory and the config files. """ - self.sa_session.clear() #this prevents the metadata reverting that has been seen in conjunction with the PBS job runner + self.sa_session.expunge_all() #this prevents the metadata reverting that has been seen in conjunction with the PBS job runner if not os.path.exists( self.working_directory ): os.mkdir( self.working_directory ) # Restore parameters from the database @@ -477,7 +477,7 @@ the contents of the output files. """ # default post job setup - self.sa_session.clear() + self.sa_session.expunge_all() job = self.sa_session.query( model.Job ).get( self.job_id ) # if the job was deleted, don't finish it if job.state == job.states.DELETED: diff -r 133252175425 -r d872c1e16afb lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/model/mapping.py Tue Nov 03 12:52:01 2009 -0500 @@ -817,7 +817,7 @@ user=relation( User, backref="roles" ), non_private_roles=relation( User, backref="non_private_roles", - primaryjoin=( ( User.table.c.id == UserRoleAssociation.table.c.user_id ) & ( UserRoleAssociation.table.c.role_id == Role.table.c.id ) & not_( Role.table.c.name == User.table.c.email & Role.table.c.type == 'private' ) ) ), + primaryjoin=( ( User.table.c.id == UserRoleAssociation.table.c.user_id ) & ( UserRoleAssociation.table.c.role_id == Role.table.c.id ) & not_( Role.table.c.name == User.table.c.email ) ) ), role=relation( Role ) ) ) @@ -1134,7 +1134,7 @@ # Pack everything into a bunch result = Bunch( **globals() ) result.engine = engine - result.flush = lambda *args, **kwargs: Session.flush( *args, **kwargs ) + # model.flush() has been removed. result.session = Session # For backward compatibility with "model.context.current" result.context = Session diff -r 133252175425 -r d872c1e16afb lib/galaxy/model/mapping_tests.py --- a/lib/galaxy/model/mapping_tests.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/model/mapping_tests.py Tue Nov 03 12:52:01 2009 -0500 @@ -19,16 +19,17 @@ d1 = model.HistoryDatasetAssociation( extension="interval", metadata=dict(chromCol=1,startCol=2,endCol=3 ), history=h2, create_dataset=True ) #h2.queries.append( q1 ) #h2.queries.append( model.Query( "h2->q2" ) ) - model.context.current.flush() - model.context.current.clear() + model.session.add_all( ( u, h1, h2, d1 ) ) + model.session.flush() + model.session.expunge_all() # Check - users = model.context.current.query( model.User ).all() + users = model.session.query( model.User ).all() assert len( users ) == 1 assert users[0].email == "james(a)foo.bar.baz" assert users[0].password == "password" assert len( users[0].histories ) == 1 assert users[0].histories[0].name == "History 1" - hists = model.context.current.query( model.History ).all() + hists = model.session.query( model.History ).all() assert hists[0].name == "History 1" assert hists[1].name == ( "H" * 255 ) assert hists[0].user == users[0] @@ -38,9 +39,9 @@ assert hists[1].datasets[0].file_name == os.path.join( "/tmp", *directory_hash_id( id ) ) + ( "/dataset_%d.dat" % id ) # Do an update and check hists[1].name = "History 2b" - model.context.current.flush() - model.context.current.clear() - hists = model.context.current.query( model.History ).all() + model.session.flush() + model.session.expunge_all() + hists = model.session.query( model.History ).all() assert hists[0].name == "History 1" assert hists[1].name == "History 2b" # gvk TODO need to ad test for GalaxySessions, but not yet sure what they should look like. diff -r 133252175425 -r d872c1e16afb lib/galaxy/model/migrate/versions/0025_user_info.py --- a/lib/galaxy/model/migrate/versions/0025_user_info.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0025_user_info.py Tue Nov 03 12:52:01 2009 -0500 @@ -21,7 +21,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" @@ -59,4 +59,4 @@ except Exception, e: log.debug( "Adding foreign key constraint 'user_form_values_id_fk' to table 'galaxy_user' failed: %s" % ( str( e ) ) ) def downgrade(): - pass \ No newline at end of file + pass diff -r 133252175425 -r d872c1e16afb lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/tools/actions/__init__.py Tue Nov 03 12:52:01 2009 -0500 @@ -235,7 +235,7 @@ # Store output out_data[ name ] = data # Store all changes to database - trans.app.model.flush() + trans.sa_session.flush() # Add all the top-level (non-child) datasets to the history for name in out_data.keys(): if name not in child_dataset_names and name not in incoming: #don't add children; or already existing datasets, i.e. async created @@ -248,7 +248,7 @@ child_dataset = out_data[ child_name ] parent_dataset.children.append( child_dataset ) # Store data after custom code runs - trans.app.model.flush() + trans.sa_session.flush() # Create the job object job = trans.app.model.Job() job.session_id = trans.get_galaxy_session().id @@ -274,7 +274,8 @@ job.add_input_dataset( name, None ) for name, dataset in out_data.iteritems(): job.add_output_dataset( name, dataset ) - trans.app.model.flush() + trans.sa_session.add( job ) + trans.sa_session.flush() # Some tools are not really executable, but jobs are still created for them ( for record keeping ). # Examples include tools that redirect to other applications ( epigraph ). These special tools must # include something that can be retrieved from the params ( e.g., REDIRECT_URL ) to keep the job diff -r 133252175425 -r d872c1e16afb lib/galaxy/tools/actions/metadata.py --- a/lib/galaxy/tools/actions/metadata.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/tools/actions/metadata.py Tue Nov 03 12:52:01 2009 -0500 @@ -26,7 +26,8 @@ job.tool_version = tool.version except: job.tool_version = "1.0.0" - job.flush() #ensure job.id is available + trans.sa_session.add( job ) + trans.sa_session.flush() #ensure job.id is available #add parameters to job_parameter table # Store original dataset state, so we can restore it. A separate table might be better (no chance of 'losing' the original state)? @@ -49,7 +50,7 @@ #Need a special state here to show that metadata is being set and also allow the job to run # i.e. if state was set to 'running' the set metadata job would never run, as it would wait for input (the dataset to set metadata on) to be in a ready state dataset.state = dataset.states.SETTING_METADATA - trans.app.model.flush() + trans.sa_session.flush() # Queue the job for execution trans.app.job_queue.put( job.id, tool ) diff -r 133252175425 -r d872c1e16afb lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/tools/actions/upload_common.py Tue Nov 03 12:52:01 2009 -0500 @@ -121,6 +121,7 @@ trans.history.add_dataset( hda, genome_build = uploaded_dataset.dbkey ) permissions = trans.app.security_agent.history_get_default_permissions( trans.history ) trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) + trans.sa_session.flush() return hda def new_library_upload( trans, uploaded_dataset, library_bunch, state=None ): @@ -291,7 +292,8 @@ for i, dataset in enumerate( data_list ): job.add_output_dataset( 'output%i' % i, dataset ) job.state = job.states.NEW - trans.app.model.flush() + trans.sa_session.add( job ) + trans.sa_session.flush() # Queue the job for execution trans.app.job_queue.put( job.id, tool ) diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/async.py --- a/lib/galaxy/web/controllers/async.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/async.py Tue Nov 03 12:52:01 2009 -0500 @@ -77,7 +77,7 @@ data.state = data.blurb = jobs.JOB_ERROR data.info = "Error -> %s" % STATUS - trans.model.flush() + trans.sa_session.flush() return "Data %s with status %s received. OK" % (data_id, STATUS) @@ -112,7 +112,7 @@ data.flush() open( data.file_name, 'wb' ).close() #create the file trans.history.add_dataset( data, genome_build=GALAXY_BUILD ) - trans.model.flush() + trans.sa_session.flush() trans.log_event( "Added dataset %d to history %d" %(data.id, trans.history.id ), tool_id=tool_id ) try: @@ -132,6 +132,6 @@ data.info = str(e) data.state = data.blurb = data.states.ERROR - trans.model.flush() + trans.sa_session.flush() return trans.fill_template('tool_executed.tmpl', out_data={}, tool=tool, config=self.app.config ) diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Tue Nov 03 12:52:01 2009 -0500 @@ -335,7 +335,7 @@ assert topmost_parent in history.datasets, "Data does not belong to current history" # Mark undeleted data.mark_undeleted() - self.app.model.flush() + trans.sa_session.flush() trans.log_event( "Dataset id %s has been undeleted" % str(id) ) return True return False @@ -407,7 +407,7 @@ hist.add_dataset( data.copy( copy_children = True ) ) if history in target_histories: refresh_frames = ['history'] - trans.app.model.flush() + trans.sa_session.flush() done_msg = "%i datasets copied to %i histories." % ( len( source_dataset_ids ) - invalid_datasets, len( target_histories ) ) trans.sa_session.refresh( history ) elif create_new_history: diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/library.py Tue Nov 03 12:52:01 2009 -0500 @@ -421,7 +421,7 @@ if trans.app.security_agent.can_modify_library_item( user, roles, ldda ): if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) - trans.app.model.flush() + trans.sa_session.flush() msg = "Data type changed for library dataset '%s'" % ldda.name messagetype = 'done' else: @@ -463,7 +463,7 @@ setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) ldda.metadata.dbkey = dbkey ldda.datatype.after_edit( ldda ) - trans.app.model.flush() + trans.sa_session.flush() msg = 'Attributes updated for library dataset %s' % ldda.name messagetype = 'done' else: @@ -486,7 +486,7 @@ setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) ldda.datatype.set_meta( ldda ) ldda.datatype.after_edit( ldda ) - trans.app.model.flush() + trans.sa_session.flush() msg = 'Attributes updated for library dataset %s' % ldda.name messagetype = 'done' else: diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/library_admin.py Tue Nov 03 12:52:01 2009 -0500 @@ -432,7 +432,7 @@ # The user clicked the Save button on the 'Change data type' form if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) - trans.app.model.flush() + trans.sa_session.flush() msg = "Data type changed for library dataset '%s'" % ldda.name return trans.fill_template( "/admin/library/ldda_edit_info.mako", ldda=ldda, @@ -469,7 +469,7 @@ setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) ldda.metadata.dbkey = dbkey ldda.datatype.after_edit( ldda ) - trans.app.model.flush() + trans.sa_session.flush() msg = 'Attributes updated for library dataset %s' % ldda.name messagetype = 'done' return trans.fill_template( "/admin/library/ldda_edit_info.mako", @@ -488,7 +488,7 @@ setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) ldda.datatype.set_meta( ldda ) ldda.datatype.after_edit( ldda ) - trans.app.model.flush() + trans.sa_session.flush() msg = 'Attributes updated for library dataset %s' % ldda.name return trans.fill_template( "/admin/library/ldda_edit_info.mako", ldda=ldda, @@ -674,6 +674,10 @@ replace_id = params.get( 'replace_id', None ) if replace_id not in [ None, 'None' ]: replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( int( replace_id ) ) + # The name is separately - by the time the new ldda is created, + # replace_dataset.name will point to the new ldda, not the one it's + # replacing. + replace_dataset_name = replace_dataset.name if not last_used_build: last_used_build = replace_dataset.library_dataset_dataset_association.dbkey # Don't allow multiple datasets to be uploaded when replacing a dataset with a new version @@ -701,7 +705,7 @@ if created_outputs: total_added = len( created_outputs.values() ) if replace_dataset: - msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset.name, folder.name ) + msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset_name, folder.name ) else: if not folder.parent: # Libraries have the same name as their root_folder diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/requests.py Tue Nov 03 12:52:01 2009 -0500 @@ -294,7 +294,7 @@ # save all the new/unsaved samples entered by the user if edit_mode == 'False': for index in range(len(current_samples)-len(request.samples)): - sample_index = index + len(request.samples) + sample_index = len(request.samples) sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) sample_values = [] for field_index in range(len(request.type.sample_form.fields)): diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/root.py Tue Nov 03 12:52:01 2009 -0500 @@ -277,7 +277,7 @@ if not __ok_to_edit_metadata( data.id ): return trans.show_error_message( "This dataset is currently being used as input or output. You cannot change datatype until the jobs have completed or you have canceled them." ) trans.app.datatypes_registry.change_datatype( data, params.datatype ) - trans.app.model.flush() + trans.sa_session.flush() else: return trans.show_error_message( "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( data.extension, params.datatype ) ) elif params.save: @@ -303,7 +303,7 @@ data.datatype.after_edit( data ) else: msg = ' (Metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata.)' - trans.app.model.flush() + trans.sa_session.flush() return trans.show_ok_message( "Attributes updated%s" % msg, refresh_frames=['history'] ) elif params.detect: # The user clicked the Auto-detect button on the 'Edit Attributes' form @@ -322,7 +322,7 @@ msg = 'Attributes updated' data.set_meta() data.datatype.after_edit( data ) - trans.app.model.flush() + trans.sa_session.flush() return trans.show_ok_message( msg, refresh_frames=['history'] ) elif params.convert_data: target_type = kwd.get("target_type", None) @@ -383,7 +383,7 @@ if job.check_if_output_datasets_deleted(): job.mark_deleted() self.app.job_manager.job_stop_queue.put( job.id ) - self.app.model.flush() + trans.sa_session.flush() @web.expose def delete( self, trans, id = None, show_deleted_on_refresh = False, **kwd): @@ -432,7 +432,7 @@ for dataset in history.datasets: dataset.deleted = True dataset.clear_associated_files() - self.app.model.flush() + trans.sa_session.flush() trans.log_event( "History id %s cleared" % (str(history.id)) ) trans.response.send_redirect( url_for("/index" ) ) @web.expose diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/tool_runner.py Tue Nov 03 12:52:01 2009 -0500 @@ -198,8 +198,6 @@ # pasted data datasets.append( create_dataset( 'Pasted Entry' ) ) break - if datasets: - trans.model.flush() return [ d.id for d in datasets ] @web.expose diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/framework/__init__.py Tue Nov 03 12:52:01 2009 -0500 @@ -139,7 +139,7 @@ self.__galaxy_session = NOT_SET base.DefaultWebTransaction.__init__( self, environ ) self.setup_i18n() - self.sa_session.clear() + self.sa_session.expunge_all() self.debug = asbool( self.app.config.get( 'debug', False ) ) # Flag indicating whether we are in workflow building mode (means # that the current history should not be used for parameter values @@ -302,12 +302,12 @@ self.galaxy_session = galaxy_session # Do we need to flush the session? if galaxy_session_requires_flush: - objects_to_flush = [ galaxy_session ] + sa_session.add( galaxy_session ) # FIXME: If prev_session is a proper relation this would not # be needed. if prev_galaxy_session: - objects_to_flush.append( prev_galaxy_session ) - sa_session.flush( objects_to_flush ) + sa_session.add( prev_galaxy_session ) + sa_session.flush() # If the old session was invalid, get a new history with our new session if invalidate_existing_session: self.new_history() @@ -427,7 +427,8 @@ if not last_accessed: # Only set default history permissions if current history is not from a previous session self.app.security_agent.history_set_default_permissions( history, dataset=True, bypass_manage_permission=True ) - self.sa_session.flush( [ prev_galaxy_session, self.galaxy_session, history ] ) + self.sa_session.add_all( ( prev_galaxy_session, self.galaxy_session, history ) ) + self.sa_session.flush() # This method is not called from the Galaxy reports, so the cookie will always be galaxysession self.__update_session_cookie( name='galaxysession' ) def handle_user_logout( self ): @@ -439,7 +440,8 @@ prev_galaxy_session = self.galaxy_session prev_galaxy_session.is_valid = False self.galaxy_session = self.__create_new_session( prev_galaxy_session ) - self.sa_session.flush( [ prev_galaxy_session, self.galaxy_session ] ) + self.sa_session.add_all( ( prev_galaxy_session, self.galaxy_session ) ) + self.sa_session.flush() # This method is not called from the Galaxy reports, so the cookie will always be galaxysession self.__update_session_cookie( name='galaxysession' ) @@ -466,7 +468,8 @@ def set_history( self, history ): if history and not history.deleted: self.galaxy_session.current_history = history - self.sa_session.flush( [ self.galaxy_session ] ) + self.sa_session.add( self.galaxy_session ) + self.sa_session.flush() history = property( get_history, set_history ) def new_history( self, name=None ): """ @@ -489,7 +492,8 @@ # Set the user's default history permissions self.app.security_agent.history_set_default_permissions( history ) # Save - self.sa_session.flush( [ self.galaxy_session, history ] ) + self.sa_session.add_all( ( self.galaxy_session, history ) ) + self.sa_session.flush() return history def get_user( self ): @@ -498,7 +502,8 @@ def set_user( self, user ): """Set the current user.""" self.galaxy_session.user = user - self.sa_session.flush( [ self.galaxy_session ] ) + self.sa_session.add( self.galaxy_session ) + self.sa_session.flush() user = property( get_user, set_user ) def get_user_and_roles( self ): diff -r 133252175425 -r d872c1e16afb test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Tue Nov 03 12:52:00 2009 -0500 +++ b/test/functional/test_forms_and_requests.py Tue Nov 03 12:52:01 2009 -0500 @@ -29,6 +29,7 @@ .filter( galaxy.model.FormDefinitionCurrent.table.c.deleted==False ) \ .order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() ) for fdc in fdc_list: + sa_session.refresh( fdc.latest_form ) if form_name == fdc.latest_form.name: return fdc.latest_form return None diff -r 133252175425 -r d872c1e16afb test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Tue Nov 03 12:52:00 2009 -0500 +++ b/test/functional/test_security_and_libraries.py Tue Nov 03 12:52:01 2009 -0500 @@ -156,7 +156,7 @@ raise AssertionError( '%s not in history id %d default_permissions after they were changed' % ( value.action, latest_history.id ) ) # Add a dataset to the history self.upload_file( '1.bed' ) - latest_dataset = galaxy.model.Dataset.query().order_by( desc( galaxy.model.Dataset.table.c.create_time ) ).first() + latest_dataset = sa_session.query( galaxy.model.Dataset ).order_by( desc( galaxy.model.Dataset.table.c.create_time ) ).first() # Make sure DatasetPermissionss are correct if len( latest_dataset.actions ) != len( latest_history.default_permissions ): raise AssertionError( '%d DatasetPermissionss were created for dataset id %d when it was created ( should have been %d )' % \ diff -r 133252175425 -r d872c1e16afb test/functional/test_user_info.py --- a/test/functional/test_user_info.py Tue Nov 03 12:52:00 2009 -0500 +++ b/test/functional/test_user_info.py Tue Nov 03 12:52:01 2009 -0500 @@ -14,6 +14,7 @@ .filter( galaxy.model.FormDefinitionCurrent.table.c.deleted==False ) \ .order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() ) for fdc in fdc_list: + sa_session.refresh( fdc.latest_form ) if form_name == fdc.latest_form.name: return fdc.latest_form return None @@ -146,4 +147,4 @@ self.visit_page('forms/manage?show_filter=Deleted') self.check_page_for_string(form_one_latest.name) self.logout() - \ No newline at end of file + diff -r 133252175425 -r d872c1e16afb tools/data_source/microbial_import_code.py --- a/tools/data_source/microbial_import_code.py Tue Nov 03 12:52:00 2009 -0500 +++ b/tools/data_source/microbial_import_code.py Tue Nov 03 12:52:01 2009 -0500 @@ -123,7 +123,7 @@ data = app.datatypes_registry.change_datatype( data, file_type ) data.init_meta() data.set_peek() - app.model.flush() + data.flush() elif fields[0] == "#NewFile": description = fields[1] chr = fields[2] @@ -137,7 +137,7 @@ newdata.flush() app.security_agent.copy_dataset_permissions( base_dataset.dataset, newdata.dataset ) history.add_dataset( newdata ) - app.model.flush() + history.flush() try: copyfile(filepath,newdata.file_name) newdata.info = newdata.name @@ -148,4 +148,4 @@ newdata.dbkey = dbkey newdata.init_meta() newdata.set_peek() - app.model.flush() + newdata.flush() diff -r 133252175425 -r d872c1e16afb tools/filters/lav_to_bed_code.py --- a/tools/filters/lav_to_bed_code.py Tue Nov 03 12:52:00 2009 -0500 +++ b/tools/filters/lav_to_bed_code.py Tue Nov 03 12:52:01 2009 -0500 @@ -16,4 +16,3 @@ data.flush() except: continue - app.model.flush() \ No newline at end of file diff -r 133252175425 -r d872c1e16afb tools/maf/maf_to_bed_code.py --- a/tools/maf/maf_to_bed_code.py Tue Nov 03 12:52:00 2009 -0500 +++ b/tools/maf/maf_to_bed_code.py Tue Nov 03 12:52:01 2009 -0500 @@ -21,7 +21,6 @@ output_data.dbkey = dbkey output_data.name = basic_name + " (" + dbkey + ")" output_data.flush() - app.model.flush() output_data_list.append(output_data) elif line.startswith("#FILE"): fields = line.split("\t") @@ -36,7 +35,6 @@ app.security_agent.copy_dataset_permissions( output_data.dataset, newdata.dataset ) newdata.flush() history.flush() - app.model.flush() try: move(filepath,newdata.file_name) newdata.info = newdata.name @@ -47,7 +45,7 @@ newdata.dbkey = dbkey newdata.init_meta() newdata.set_peek() - app.model.flush() + newdata.flush() output_data_list.append(newdata) else: new_stdout = new_stdout + line

1 0

[hg] galaxy 2952: Fix a bug in streaming library tarballs. Quot...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/6491acd0bef2 changeset: 2952:6491acd0bef2 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Nov 03 15:39:51 2009 -0500 description: Fix a bug in streaming library tarballs. Quoth James: This bears repeating (heh, again... -nate) -- NEVER use a mutable object (like a dict) as a function parameter default. The default is evaluated once (at def time) and then used for every call to the function. This is really bad since every call, across multiple thread, are writing to that one dict. In this case, it resulted in the values of parameters that have dependencies being persisted across requests. Took me three solid days to find! diffstat: lib/galaxy/util/streamball.py | 6 ++++-- 1 files changed, 4 insertions(+), 2 deletions(-) diffs (17 lines): diff -r 2300a80d80e5 -r 6491acd0bef2 lib/galaxy/util/streamball.py --- a/lib/galaxy/util/streamball.py Tue Nov 03 13:04:35 2009 -0500 +++ b/lib/galaxy/util/streamball.py Tue Nov 03 15:39:51 2009 -0500 @@ -7,9 +7,11 @@ log = logging.getLogger( __name__ ) class StreamBall( object ): - def __init__( self, mode, members={} ): + def __init__( self, mode, members=None ): + self.members = members + if members is None: + self.members = {} self.mode = mode - self.members = members self.wsgi_status = None self.wsgi_headeritems = None def add( self, file, relpath ):

1 0

[hg] galaxy 2953: Added 'History' column to HDA grid.
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/14e178f656ba changeset: 2953:14e178f656ba user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Nov 03 16:53:14 2009 -0500 description: Added 'History' column to HDA grid. diffstat: lib/galaxy/web/controllers/dataset.py | 26 +++++++++++++++++++------- templates/dataset/grid.mako | 11 ++++++++--- templates/root/history_common.mako | 2 +- 3 files changed, 28 insertions(+), 11 deletions(-) diffs (116 lines): diff -r 6491acd0bef2 -r 14e178f656ba lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Tue Nov 03 15:39:51 2009 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Tue Nov 03 16:53:14 2009 -0500 @@ -45,6 +45,11 @@ """ class HistoryDatasetAssociationListGrid( grids.Grid ): + # Custom columns for grid. + class HistoryColumn( grids.GridColumn ): + def get_value( self, trans, grid, hda): + return hda.history.name + class StatusColumn( grids.GridColumn ): def get_value( self, trans, grid, hda ): if hda.deleted: @@ -52,6 +57,7 @@ return "" def get_link( self, trans, grid, hda ): return None + class TagsColumn( grids.GridColumn ): def __init__(self, col_name, key, filterable): grids.GridColumn.__init__(self, col_name, key=key, filterable=filterable) @@ -107,14 +113,16 @@ return accepted_filters # Grid definition - title = "Stored Datasets" + title = "Saved Datasets" model_class = model.HistoryDatasetAssociation template='/dataset/grid.mako' default_sort_key = "-create_time" columns = [ - grids.GridColumn( "Name", key="name", - # Link name to dataset's history. + grids.GridColumn( "Name", key="name", + # Link name to dataset's history. link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ) ), + HistoryColumn( "History", key="history", + link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ), TagsColumn( "Tags", key="tags", filterable=True ), StatusColumn( "Status", key="deleted", attach_popup=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), @@ -285,8 +293,9 @@ log.warn( "Invalid history_dataset_association id '%r' passed to list", hda_id ) if hdas: - - if operation == "switch": + if operation == "switch" or operation == "switch_history": + # Switch to a history that the HDA resides in. + # Convert hda to histories. histories = [] for hda in hdas: @@ -295,8 +304,11 @@ # Use history controller to switch the history. TODO: is this reasonable? status, message = trans.webapp.controllers['history']._list_switch( trans, histories ) - # Current history changed, refresh history frame - trans.template_context['refresh_frames'] = ['history'] + # Current history changed, refresh history frame; if switching to a dataset, set hda seek. + trans.template_context['refresh_frames'] = ['history'] + if operation == "switch": + hda_ids = [ trans.security.encode_id( hda.id ) for hda in hdas ] + trans.template_context[ 'seek_hda_ids' ] = hda_ids # Render the list view return self.stored_list_grid( trans, status=status, message=message, **kwargs ) diff -r 6491acd0bef2 -r 14e178f656ba templates/dataset/grid.mako --- a/templates/dataset/grid.mako Tue Nov 03 15:39:51 2009 -0500 +++ b/templates/dataset/grid.mako Tue Nov 03 16:53:14 2009 -0500 @@ -92,8 +92,6 @@ t.autocomplete("${h.url_for( controller='tag', action='tag_autocomplete_data', item_class='HistoryDatasetAssociation' )}", autocomplete_options); - //t.addClass("tag-input"); - return t; }); ## Can this be moved into base.mako? @@ -110,7 +108,14 @@ %endif %if 'history' in refresh_frames: if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history', hda_id=str(ids) )}"; + ## If available, include HDA ids to seek to in history request. + <% + hda_id = None + if seek_hda_ids: + hda_id = str( seek_hda_ids[0] ) # Use only the first id. + print hda_id + %> + parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history', hda_id=hda_id )}"; if ( parent.force_right_panel ) { parent.force_right_panel( 'show' ); } diff -r 6491acd0bef2 -r 14e178f656ba templates/root/history_common.mako --- a/templates/root/history_common.mako Tue Nov 03 15:39:51 2009 -0500 +++ b/templates/root/history_common.mako Tue Nov 03 16:53:14 2009 -0500 @@ -1,6 +1,7 @@ <% _=n_ %> ## Render the dataset `data` as history item, using `hid` as the displayed id <%def name="render_dataset( data, hid, show_deleted_on_refresh = False, user_owns_dataset = True )"> + <a name="${trans.security.encode_id( data.id )}"></a> <% if data.state in ['no state','',None]: data_state = "queued" @@ -21,7 +22,6 @@ %endif ## Header row for history items (name, state, action buttons) - <a name="${trans.security.encode_id(data.id)}"></a> <div style="overflow: hidden;" class="historyItemTitleBar"> <div class="historyItemButtons"> %if data_state == "upload":

1 0

[hg] galaxy 2954: History ordering bug with SQLAlchemy 0.5 (deve...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/46791b5a653b changeset: 2954:46791b5a653b user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Nov 03 17:16:40 2009 -0500 description: History ordering bug with SQLAlchemy 0.5 (developers - queries are no longer ordered by primary key by default, so order explicitly if it matters) and a <model_object>.c that slipped through. diffstat: lib/galaxy/jobs/__init__.py | 2 +- lib/galaxy/web/controllers/root.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diffs (25 lines): diff -r 14e178f656ba -r 46791b5a653b lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Tue Nov 03 16:53:14 2009 -0500 +++ b/lib/galaxy/jobs/__init__.py Tue Nov 03 17:16:40 2009 -0500 @@ -174,7 +174,7 @@ if self.track_jobs_in_database: for j in self.sa_session.query( model.Job ) \ .options( lazyload( "external_output_metadata" ), lazyload( "parameters" ) ) \ - .filter( model.Job.c.state == model.Job.states.NEW ): + .filter( model.Job.state == model.Job.states.NEW ): job = JobWrapper( j, self.app.toolbox.tools_by_id[ j.tool_id ], self ) new_jobs.append( job ) else: diff -r 14e178f656ba -r 46791b5a653b lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Tue Nov 03 16:53:14 2009 -0500 +++ b/lib/galaxy/web/controllers/root.py Tue Nov 03 17:16:40 2009 -0500 @@ -72,7 +72,8 @@ .filter( model.HistoryDatasetAssociation.history == history ) \ .options( eagerload( "children" ) ) \ .join( "dataset" ).filter( model.Dataset.purged == False ) \ - .options( eagerload_all( "dataset.actions" ) ) + .options( eagerload_all( "dataset.actions" ) ) \ + .order_by( model.HistoryDatasetAssociation.hid ) if not show_deleted: query = query.filter( model.HistoryDatasetAssociation.deleted == False ) return trans.stream_template_mako( "root/history.mako",

1 0

[hg] galaxy 2955: trackster: much greater resolution for line tr...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d7c66019de13 changeset: 2955:d7c66019de13 user: Kanwei Li <kanwei(a)gmail.com> date: Tue Nov 03 19:16:01 2009 -0500 description: trackster: much greater resolution for line tracks (might still need to tweak BLOCK_SIZE), fixed stacking issue in feature tracks for features sharing same name) diffstat: lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py | 4 +- lib/galaxy/visualization/tracks/data/array_tree.py | 45 ++++++----- lib/galaxy/visualization/tracks/data/interval_index.py | 6 +- lib/galaxy/web/controllers/tracks.py | 6 +- static/scripts/trackster.js | 46 +++++++---- static/trackster.css | 1 + templates/tracks/browser.mako | 1 + 7 files changed, 65 insertions(+), 44 deletions(-) diffs (293 lines): diff -r 46791b5a653b -r d7c66019de13 lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py --- a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py Tue Nov 03 17:16:40 2009 -0500 +++ b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py Tue Nov 03 19:16:01 2009 -0500 @@ -8,6 +8,8 @@ from bx.arrays.array_tree import * from bx.arrays.wiggle import IntervalReader +BLOCK_SIZE = 1000 + def main(): input_fname = sys.argv[1] @@ -16,7 +18,7 @@ reader = IntervalReader( open( input_fname ) ) # Fill array from wiggle - d = array_tree_dict_from_wiggle_reader( reader, {} ) + d = array_tree_dict_from_wiggle_reader( reader, {}, block_size = BLOCK_SIZE ) for value in d.itervalues(): value.root.build_summary() diff -r 46791b5a653b -r d7c66019de13 lib/galaxy/visualization/tracks/data/array_tree.py --- a/lib/galaxy/visualization/tracks/data/array_tree.py Tue Nov 03 17:16:40 2009 -0500 +++ b/lib/galaxy/visualization/tracks/data/array_tree.py Tue Nov 03 19:16:01 2009 -0500 @@ -31,11 +31,16 @@ f.close() return { 'max': float( max(root_summary.maxs) ), 'min': float( min(root_summary.mins) ) } - def get_data( self, chrom, start, end ): + def get_data( self, chrom, start, end, **kwargs ): start = int( start ) end = int( end ) - level = int( ceil( log( end - start, BLOCK_SIZE ) ) ) - 1 - + resolution = max(1, ceil(float(kwargs['resolution']))) + + level = int( floor( log( resolution, BLOCK_SIZE ) ) ) + level = max( level, 0 ) + stepsize = BLOCK_SIZE ** level + step1 = stepsize * BLOCK_SIZE + # Open the file f = open( self.dataset.file_name ) d = FileArrayTreeDict( f ) @@ -47,22 +52,20 @@ # Is the requested level valid? assert 0 <= level <= chrom_array_tree.levels # Calculate the actual start/range/step of the block we're getting - size = BLOCK_SIZE ** (level+1) - block_start = ( start // BLOCK_SIZE ) * BLOCK_SIZE - block_step = size // BLOCK_SIZE - indexes = range( block_start, block_start + size, block_step ) - # Return either data point or a summary depending on the level - if level > 0: - s = chrom_array_tree.get_summary( start, level ) - f.close() - if s is not None: - return zip( indexes, map( float, s.sums / s.counts ) ) + + results = [] + for block_start in range( start, end, stepsize * BLOCK_SIZE ): + # print block_start + # Return either data point or a summary depending on the level + indexes = range( block_start, block_start + stepsize * BLOCK_SIZE, stepsize ) + if level > 0: + s = chrom_array_tree.get_summary( block_start, level ) + if s is not None: + results.extend( zip( indexes, map( float, s.sums / s.counts ) ) ) else: - return None - else: - v = chrom_array_tree.get_leaf( start ) - f.close() - if v is not None: - return zip( indexes, map( float, v ) ) - else: - return None \ No newline at end of file + v = chrom_array_tree.get_leaf( block_start ) + if v is not None: + results.extend( zip( indexes, map( float, v ) ) ) + + f.close() + return results diff -r 46791b5a653b -r d7c66019de13 lib/galaxy/visualization/tracks/data/interval_index.py --- a/lib/galaxy/visualization/tracks/data/interval_index.py Tue Nov 03 17:16:40 2009 -0500 +++ b/lib/galaxy/visualization/tracks/data/interval_index.py Tue Nov 03 19:16:01 2009 -0500 @@ -11,17 +11,18 @@ self.original_dataset = original_dataset self.converted_dataset = converted_dataset - def get_data( self, chrom, start, end ): + def get_data( self, chrom, start, end, **kwargs ): start, end = int(start), int(end) chrom = str(chrom) source = open( self.original_dataset.file_name ) index = Indexes( self.converted_dataset.file_name ) results = [] + uid = 0 for start, end, offset in index.find(chrom, start, end): source.seek(offset) feature = source.readline().split() - payload = { 'start': start, 'end': end, 'name': feature[3] } + payload = { 'uid': uid, 'start': start, 'end': end, 'name': feature[3] } try: payload['strand'] = feature[5] except IndexError: @@ -41,5 +42,6 @@ pass results.append(payload) + uid += 1 return results diff -r 46791b5a653b -r d7c66019de13 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Tue Nov 03 17:16:40 2009 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Tue Nov 03 19:16:01 2009 -0500 @@ -184,7 +184,7 @@ return manifest @web.json - def data( self, trans, dataset_id, track_type, chrom, low, high, stats=False ): + def data( self, trans, dataset_id, track_type, chrom, low, high, **kwargs ): """ Called by the browser to request a block of data """ @@ -216,10 +216,10 @@ data_provider = dataset_type_to_data_provider[ converted_dataset_type ]( converted_dataset, dataset ) # Return stats if we need them - if stats: return data_provider.get_stats( chrom ) + if 'stats' in kwargs: return data_provider.get_stats( chrom ) # Get the requested chunk of data - return data_provider.get_data( chrom, low, high ) + return data_provider.get_data( chrom, low, high, **kwargs ) def __dataset_as_type( self, trans, dataset, type ): """ diff -r 46791b5a653b -r d7c66019de13 static/scripts/trackster.js --- a/static/scripts/trackster.js Tue Nov 03 17:16:40 2009 -0500 +++ b/static/scripts/trackster.js Tue Nov 03 19:16:01 2009 -0500 @@ -1,13 +1,15 @@ /* Trackster 2009, James Taylor, Kanwei Li */ +var DEBUG = false; var DENSITY = 1000, DATA_ERROR = "There was an error in indexing this dataset.", DATA_NONE = "No data for this chrom/contig.", DATA_PENDING = "Currently indexing... please wait", DATA_LOADING = "Loading data...", - CACHED_TILES = 10, + CACHED_TILES_FEATURE = 10, + CACHED_TILES_LINE = 30, CACHED_DATA = 20, CONTEXT = $("<canvas></canvas>").get(0).getContext("2d"), RIGHT_STRAND, LEFT_STRAND; @@ -104,6 +106,9 @@ this.high = Math.ceil(high); this.center = Math.round( this.low + (this.high - this.low) / 2 ); + // 10^log10(range / DENSITY) Close approximation for browser window, assuming DENSITY = window width + this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / DENSITY ) / Math.LN10 ) ); + // Overview $("#overview-box").css( { left: ( this.low / this.span ) * $("#overview-viewport").width(), @@ -157,18 +162,16 @@ }); var TiledTrack = function() { - this.tile_cache = new Cache(CACHED_TILES); - // this.tile_cache = {}; }; $.extend( TiledTrack.prototype, Track.prototype, { draw: function() { var low = this.view.low, high = this.view.high, - range = high - low; - - var resolution = Math.pow( 10, Math.ceil( Math.log( range / DENSITY ) / Math.log( 10 ) ) ); - resolution = Math.max( resolution, 0.1 ); - resolution = Math.min( resolution, 1000000 ); + range = high - low, + resolution = this.view.resolution; + + + if (DEBUG) { $("#debug").text(resolution); } var parent_element = $("<div style='position: relative;'></div>"); this.content_div.children( ":first" ).remove(); @@ -187,7 +190,7 @@ // console.log("cached tile " + tile_index); var tile_low = tile_index * DENSITY * resolution; cached.css( { - left: ( tile_low - this.view.low ) * w_scale + left: ( tile_low - low ) * w_scale }); // Our responsibility to move the element to the new parent parent_element.append( cached ); @@ -229,6 +232,7 @@ }); var LineTrack = function ( name, dataset_id, height ) { + this.tile_cache = new Cache(CACHED_TILES_LINE); Track.call( this, name, $("#viewport") ); TiledTrack.call( this ); @@ -236,6 +240,7 @@ this.height_px = (height ? height : 100); this.container_div.addClass( "line-track" ); this.dataset_id = dataset_id; + this.data_queue = {}; this.cache = new Cache(CACHED_DATA); // We need to cache some data because of // asynchronous calls }; @@ -282,11 +287,17 @@ low = position * DENSITY * resolution, high = ( position + 1 ) * DENSITY * resolution, key = resolution + "_" + position; - - $.getJSON( data_url, { track_type: this.track_type, chrom: this.view.chrom, low: low, high: high, dataset_id: this.dataset_id }, function ( data ) { - track.cache[key] = data; - $(document).trigger( "redraw" ); - }); + + if (!track.data_queue[key]) { + track.data_queue[key] = true; + $.getJSON( data_url, { track_type: this.track_type, chrom: this.view.chrom, + low: low, high: high, dataset_id: this.dataset_id, + resolution: this.view.resolution }, function ( data ) { + track.cache[key] = data; + delete track.data_queue[key]; + track.draw(); + }); + } }, draw_tile: function( resolution, tile_index, parent_element, w_scale ) { if (!this.vertical_range) { // We don't have the necessary information yet @@ -340,6 +351,7 @@ }); var FeatureTrack = function ( name, dataset_id, height ) { + this.tile_cache = new Cache(CACHED_TILES_FEATURE); Track.call( this, name, $("#viewport") ); TiledTrack.call( this ); @@ -409,9 +421,9 @@ if (end_ary[j] === undefined || end_ary[j] < f_start) { end_ary[j] = f_end; if (include_labels) { - this.zi_slots[feature.name] = j; + this.zi_slots[feature.uid] = j; } else { - this.zo_slots[feature.name] = j; + this.zo_slots[feature.uid] = j; } break; } @@ -466,7 +478,7 @@ if (feature.start <= tile_high && feature.end >= tile_low) { var f_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ), - y_center = this.slots[feature.name] * this.vertical_gap; + y_center = this.slots[feature.uid] * this.vertical_gap; var thickness, y_start, thick_start = null, thick_end = null; if (feature.thick_start && feature.thick_end) { diff -r 46791b5a653b -r d7c66019de13 static/trackster.css --- a/static/trackster.css Tue Nov 03 17:16:40 2009 -0500 +++ b/static/trackster.css Tue Nov 03 19:16:01 2009 -0500 @@ -25,6 +25,7 @@ font-size: 100%; } +/*canvas{ border-right: 1px solid red; } /* debugging */ #nav { padding: 0.5em 0; background:#cccccc; diff -r 46791b5a653b -r d7c66019de13 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Tue Nov 03 17:16:40 2009 -0500 +++ b/templates/tracks/browser.mako Tue Nov 03 19:16:01 2009 -0500 @@ -122,6 +122,7 @@ <a href="#" onclick="javascript:view.zoom_in();view.redraw();">+</a> <a href="#" onclick="javascript:view.zoom_out();view.redraw();">-</a> </form> + <div id="debug" style="float: right"></div> </div> </div> </div>

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[hg] galaxy 2956: When reseting password, if an email has not ye...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/984b1eb6c428 changeset: 2956:984b1eb6c428 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Nov 04 09:32:09 2009 -0500 description: When reseting password, if an email has not yet been provided, make text box empty and not contain 'None' diffstat: lib/galaxy/web/controllers/user.py | 2 ++ 1 files changed, 2 insertions(+), 0 deletions(-) diffs (12 lines): diff -r d7c66019de13 -r 984b1eb6c428 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Tue Nov 03 19:16:01 2009 -0500 +++ b/lib/galaxy/web/controllers/user.py Wed Nov 04 09:32:09 2009 -0500 @@ -571,6 +571,8 @@ return trans.show_ok_message( "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( email, web.url_for( action='login' ) ) ) elif email != None: error = "The specified user does not exist" + elif email is None: + email = "" return trans.show_form( web.FormBuilder( web.url_for(), "Reset Password", submit_text="Submit" ) .add_text( "email", "Email", value=email, error=error ) )

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