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commit/galaxy-central: greg: Add functional tests to cover some recent new library features, and a couple of miscellaneous UI improvements.
by Bitbucket 09 Mar '11

09 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ba87157587e0/ changeset: r5204:ba87157587e0 user: greg date: 2011-03-09 20:50:54 summary: Add functional tests to cover some recent new library features, and a couple of miscellaneous UI improvements. affected #: 5 files (8.5 KB) --- a/lib/galaxy/web/controllers/library_common.py Wed Mar 09 14:22:10 2011 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Wed Mar 09 14:50:54 2011 -0500 @@ -2132,7 +2132,8 @@ def __build_target_folder_id_select_field( trans, folders, selected_value='none' ): for folder in folders: if not folder.parent: - folder.name = 'Data library root folder' + folder.name = 'Data library root' + break return build_select_field( trans, objs=folders, label_attr='name', --- a/lib/galaxy/web/controllers/requests_common.py Wed Mar 09 14:22:10 2011 -0500 +++ b/lib/galaxy/web/controllers/requests_common.py Wed Mar 09 14:50:54 2011 -0500 @@ -1636,9 +1636,11 @@ else: selected_folder_id = 'none' folders = [] - # TODO: Change the name of the library root folder to "Library root" to clarify to the - # user that it is the root folder. We probably should just change this in the Library code, - # and update the data in the db. + # Change the name of the library root folder to clarify that it is the root + for folder in folders: + if not folder.parent: + folder.name = 'Data library root' + break folder_select_field = build_select_field( trans, folders, 'name', --- a/templates/library/common/move_library_item.mako Wed Mar 09 14:22:10 2011 -0500 +++ b/templates/library/common/move_library_item.mako Wed Mar 09 14:50:54 2011 -0500 @@ -1,6 +1,16 @@ <%namespace file="/message.mako" import="render_msg" /><%inherit file="/base.mako"/> +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js("jquery.autocomplete", "autocomplete_tagging" )} +</%def> + +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "autocomplete_tagging" )} +</%def> + <% if source_library: source_library_id = trans.security.encode_id( source_library.id ) --- a/test/base/twilltestcase.py Wed Mar 09 14:22:10 2011 -0500 +++ b/test/base/twilltestcase.py Wed Mar 09 14:50:54 2011 -0500 @@ -2144,7 +2144,8 @@ #tc.fv( "1", "do_action", format ) #tc.submit( "action_on_datasets_button" ) # Here's the new approach... - url = "%s/library_common/act_on_multiple_datasets?cntrller=%s&library_id=%s&do_action=%s" % ( self.url, cntrller, library_id, format ) + url = "%s/library_common/act_on_multiple_datasets?cntrller=%s&library_id=%s&do_action=%s" \ + % ( self.url, cntrller, library_id, format ) for ldda_id in ldda_ids: url += "&ldda_ids=%s" % ldda_id self.visit_url( url ) @@ -2195,6 +2196,21 @@ errmsg += 'Unpacked archive remains in: %s\n' % tmpd raise AssertionError( errmsg ) shutil.rmtree( tmpd ) + def move_library_item( self, cntrller, item_type, item_id, source_library_id, make_target_current, + target_library_id='', target_folder_id='', strings_displayed=[], strings_displayed_after_submit=[] ): + self.home() + self.visit_url( "%s/library_common/move_library_item?cntrller=%s&item_type=%s&item_id=%s&source_library_id=%s&make_target_current=%s" \ + % ( self.url, cntrller, item_type, item_id, source_library_id, make_target_current ) ) + if target_library_id: + self.refresh_form( 'target_library_id', target_library_id ) + if target_folder_id: + tc.fv( '1', 'target_folder_id', target_folder_id ) + for check_str in strings_displayed: + self.check_page_for_string( check_str ) + tc.submit( 'move_library_item_button' ) + for check_str in strings_displayed_after_submit: + self.check_page_for_string( check_str ) + self.home() def delete_library_item( self, cntrller, library_id, item_id, item_name, item_type='library_dataset' ): """Mark a library item as deleted""" self.home() --- a/test/functional/test_library_features.py Wed Mar 09 14:22:10 2011 -0500 +++ b/test/functional/test_library_features.py Wed Mar 09 14:50:54 2011 -0500 @@ -35,7 +35,7 @@ def test_005_create_libraries( self ): """Testing creating libraries used in this script, then renaming one of them""" # Logged in as admin_user - for index in range( 0, 1 ): + for index in range( 0, 3 ): name = 'library%s' % str( index + 1 ) description = '%s description' % name synopsis = '%s synopsis' % name @@ -45,6 +45,12 @@ global library1 library1 = get_library( 'library1', 'library1 description', 'library1 synopsis' ) assert library1 is not None, 'Problem retrieving library (library1) from the database' + global library2 + library2 = get_library( 'library2', 'library2 description', 'library2 synopsis' ) + assert library2 is not None, 'Problem retrieving library (library2) from the database' + global library3 + library3 = get_library( 'library3', 'library3 description', 'library3 synopsis' ) + assert library3 is not None, 'Problem retrieving library (library3) from the database' # Rename the library new_name = "library1 new name" new_description = "library1 new description" @@ -413,13 +419,128 @@ raise AssertionError( 'The library_dataset id %s named "%s" has not been marked as deleted.' % \ ( str( library_dataset.id ), library_dataset.name ) ) check_folder( library1.root_folder ) + def test_120_populate_public_library2( self ): + """Testing library datasets within a library""" + # Logged in as admin_user + # Add a folder named Three to library2 root + root_folder = library2.root_folder + name = "One" + description = "One description" + self.add_folder( 'library_admin', + self.security.encode_id( library2.id ), + self.security.encode_id( root_folder.id ), + name=name, + description=description ) + global folder3 + folder3 = get_folder( root_folder.id, name, description ) + assert folder3 is not None, 'Problem retrieving library folder named "%s" from the database' % name + # Upload dataset 1.bed to folder One + filename = '1.bed' + ldda_message = "Testing uploading %s" % filename + self.upload_library_dataset( cntrller='library_admin', + library_id=self.security.encode_id( library2.id ), + folder_id=self.security.encode_id( folder3.id ), + filename=filename, + file_type='bed', + dbkey='hg18', + ldda_message=ldda_message, + strings_displayed=[ 'Upload files' ] ) + global ldda5 + ldda5 = get_latest_ldda_by_name( filename ) + assert ldda5 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda5 from the database' + # Add a sub-folder named Two to folder One + name = "Two" + description = "Two description" + self.add_folder( 'library_admin', + self.security.encode_id( library2.id ), + self.security.encode_id( folder3.id ), + name=name, + description=description ) + global folder4 + folder4 = get_folder( folder3.id, name, description ) + assert folder4 is not None, 'Problem retrieving library folder named "%s" from the database' % name + # Upload dataset 2.bed to folder Two + filename = '2.bed' + ldda_message = "Testing uploading %s" % filename + self.upload_library_dataset( cntrller='library_admin', + library_id=self.security.encode_id( library2.id ), + folder_id=self.security.encode_id( folder4.id ), + filename=filename, + file_type='bed', + dbkey='hg18', + ldda_message=ldda_message, + strings_displayed=[ 'Upload files' ] ) + global ldda6 + ldda6 = get_latest_ldda_by_name( filename ) + assert ldda6 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda6 from the database' + # Add a folder named Three to library2 root + name = "Three" + description = "Three description" + self.add_folder( 'library_admin', + self.security.encode_id( library2.id ), + self.security.encode_id( root_folder.id ), + name=name, + description=description ) + global folder5 + folder5 = get_folder( root_folder.id, name, description ) + assert folder5 is not None, 'Problem retrieving library folder named "%s" from the database' % name + # Upload dataset 3.bed to library2 root folder + filename = '3.bed' + ldda_message = "Testing uploading %s" % filename + self.upload_library_dataset( cntrller='library_admin', + library_id=self.security.encode_id( library2.id ), + folder_id=self.security.encode_id( root_folder.id ), + filename=filename, + file_type='bed', + dbkey='hg18', + ldda_message=ldda_message, + strings_displayed=[ 'Upload files' ] ) + global ldda7 + ldda7 = get_latest_ldda_by_name( filename ) + assert ldda7 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda7 from the database' + def test_125_move_dataset_within_library2( self ): + """Testing moving a dataset within library2""" + # Logged in as admin_user + # Move 3.bed to folder Three + self.move_library_item( cntrller='library_admin', + item_type='ldda', + item_id=self.security.encode_id( ldda7.id ), + source_library_id=self.security.encode_id( library2.id ), + make_target_current=True, + target_folder_id=self.security.encode_id( folder5.id ), + strings_displayed=[ 'Move data library items', + '3.bed' ], + strings_displayed_after_submit=[ '1 dataset moved to folder (Three) within data library (library2)' ] ) + def test_130_move_folder_to_another_library( self ): + """Testing moving a folder to another library""" + # Logged in as admin_user + # Move folder Three which now includes 3.bed to library3 + self.move_library_item( cntrller='library_admin', + item_type='folder', + item_id=self.security.encode_id( folder5.id ), + source_library_id=self.security.encode_id( library2.id ), + make_target_current=False, + target_library_id=self.security.encode_id( library3.id ), + target_folder_id=self.security.encode_id( library3.root_folder.id ), + strings_displayed=[ 'Move data library items', + 'Three' ], + strings_displayed_after_submit=[ 'Moved folder (Three) to folder (library3) within data library (library3)' ] ) + # Make sure folder Three is not longer in library2 + self.browse_library( cntrller='library_admin', + library_id=self.security.encode_id( library2.id ), + strings_displayed=[ folder4.name, folder4.description ], + strings_not_displayed=[ folder5.name, folder5.description ] ) + # Make sure folder Three was moved to library3 + self.browse_library( cntrller='library_admin', + library_id=self.security.encode_id( library3.id ), + strings_displayed=[ folder5.name, folder5.description, ldda7.name ] ) def test_999_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" # Logged in as admin_user ################## # Purge all libraries ################## - for library in [ library1 ]: + for library in [ library1, library2, library3 ]: self.delete_library_item( 'library_admin', self.security.encode_id( library.id ), self.security.encode_id( library.id ), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Fix bugs in GFFReaderWrapper so that GFF3 files are read properly. Add GFF3 test to gff_filter_by_feature_count.
by Bitbucket 09 Mar '11

09 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/917fe1e0356e/ changeset: r5203:917fe1e0356e user: jgoecks date: 2011-03-09 20:22:10 summary: Fix bugs in GFFReaderWrapper so that GFF3 files are read properly. Add GFF3 test to gff_filter_by_feature_count. affected #: 4 files (903 bytes) --- a/lib/galaxy/datatypes/util/gff_util.py Tue Mar 08 19:01:59 2011 -0500 +++ b/lib/galaxy/datatypes/util/gff_util.py Wed Mar 09 14:22:10 2011 -0500 @@ -12,8 +12,18 @@ """ def __init__( self, reader, fields, chrom_col, feature_col, start_col, end_col, \ strand_col, score_col, default_strand, fix_strand=False, raw_line='' ): + # HACK: GFF format allows '.' for strand but GenomicInterval does not. To get around this, + # temporarily set strand and then unset after initing GenomicInterval. + unknown_strand = False + if not fix_strand and fields[ strand_col ] == '.': + unknown_strand = True + fields[ strand_col ] = '+' GenomicInterval.__init__( self, reader, fields, chrom_col, start_col, end_col, strand_col, \ default_strand, fix_strand=fix_strand ) + if unknown_strand: + self.strand = '.' + self.fields[ strand_col ] = '.' + # Handle feature, score column. self.feature_col = feature_col if self.feature_col >= self.nfields: @@ -40,13 +50,10 @@ self.intervals = intervals # Use intervals to set feature attributes. for interval in self.intervals: - # Error checking. + # Error checking. NOTE: intervals need not share the same strand. if interval.chrom != self.chrom: - raise ValueError( "interval chrom does not match self chrom: %i != %i" % \ + raise ValueError( "interval chrom does not match self chrom: %s != %s" % \ ( interval.chrom, self.chrom ) ) - if interval.strand != self.strand: - raise ValueError( "interval strand does not match self strand: %s != %s" % \ - ( interval.strand, self.strand ) ) # Set start, end of interval. if interval.start < self.start: self.start = interval.start @@ -140,7 +147,7 @@ # For debugging, uncomment this to propogate parsing exceptions up. # I.e. the underlying reason for an unexpected StopIteration exception # can be found by uncommenting this. - # raise e + #raise e # # Get next GFFFeature @@ -163,7 +170,7 @@ # Initialize feature name from seed. feature_group = self.seed_interval.attributes.get( 'group', None ) # For GFF - feature_id = self.seed_interval.attributes.get( 'id', None ) # For GFF3 + feature_id = self.seed_interval.attributes.get( 'ID', None ) # For GFF3 feature_gene_id = self.seed_interval.attributes.get( 'gene_id', None ) # For GTF feature_transcript_id = self.seed_interval.attributes.get( 'transcript_id', None ) # For GTF @@ -183,11 +190,14 @@ # If interval not associated with feature, break. group = interval.attributes.get( 'group', None ) + # GFF test: if group and feature_group != group: break - id = interval.attributes.get( 'id', None ) - if id and feature_id != id: + # GFF3 test: + parent = interval.attributes.get( 'Parent', None ) + if feature_id and feature_id != parent: break + # GTF test: gene_id = interval.attributes.get( 'gene_id', None ) transcript_id = interval.attributes.get( 'transcript_id', None ) if ( transcript_id and transcript_id != feature_transcript_id ) or \ --- a/tools/filters/gff/gff_filter_by_feature_count.py Tue Mar 08 19:01:59 2011 -0500 +++ b/tools/filters/gff/gff_filter_by_feature_count.py Wed Mar 09 14:22:10 2011 -0500 @@ -8,8 +8,7 @@ import sys from galaxy import eggs from galaxy.datatypes.util.gff_util import GFFReaderWrapper - -assert sys.version_info[:2] >= ( 2, 4 ) +from bx.intervals.io import GenomicInterval # Valid operators, ordered so that complex operators (e.g. '>=') are # recognized before simple operators (e.g. '>') @@ -62,7 +61,9 @@ skipped_lines = 0 first_skipped_line = 0 out = open( output_name, 'w' ) - for i, feature in enumerate( GFFReaderWrapper( open( input_name ), fix_strand=True ) ): + for i, feature in enumerate( GFFReaderWrapper( open( input_name ) ) ): + if not isinstance( feature, GenomicInterval ): + continue count = 0 for interval in feature.intervals: if interval.feature == feature_name: @@ -73,6 +74,9 @@ out.write( "\t".join(interval.fields) + '\n' ) kept_features += 1 + # Needed because i is 0-based but want to display stats using 1-based. + i += 1 + # Clean up. out.close() info_msg = "%i of %i features kept (%.2f%%) using condition %s. " % \ --- a/tools/filters/gff/gff_filter_by_feature_count.xml Tue Mar 08 19:01:59 2011 -0500 +++ b/tools/filters/gff/gff_filter_by_feature_count.xml Wed Mar 09 14:22:10 2011 -0500 @@ -20,12 +20,20 @@ <data format="input" name="out_file1" metadata_source="input_file1"/></outputs><tests> - <test> - <param name="input_file1" value="gops_subtract_in1.gff"/> - <param name="feature_name" value="exon"/> - <param name="cond" value=">1"/> - <output name="out_file1" file="gff_filter_by_feature_count_out1.gff"/> - </test> +  + <test> + <param name="input_file1" value="gops_subtract_in1.gff"/> + <param name="feature_name" value="exon"/> + <param name="cond" value=">1"/> + <output name="out_file1" file="gff_filter_by_feature_count_out1.gff"/> + </test> +  + <test> + <param name="input_file1" value="5.gff3"/> + <param name="feature_name" value="HSP"/> + <param name="cond" value=">=5"/> + <output name="out_file1" file="gff_filter_by_feature_count_out2.gff"/> + </test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Use GFFReaderWrapper in gff_filter_by_feature_count tool in order to leverage support for GTF, GFF, and GFF3 found in reader wrapper. This also simplifies the tool considerably.
by Bitbucket 09 Mar '11

09 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c9e6bc81817a/ changeset: r5202:c9e6bc81817a user: jgoecks date: 2011-03-09 01:01:59 summary: Use GFFReaderWrapper in gff_filter_by_feature_count tool in order to leverage support for GTF, GFF, and GFF3 found in reader wrapper. This also simplifies the tool considerably. affected #: 2 files (2.7 KB) --- a/lib/galaxy/datatypes/util/gff_util.py Tue Mar 08 16:17:09 2011 -0500 +++ b/lib/galaxy/datatypes/util/gff_util.py Tue Mar 08 19:01:59 2011 -0500 @@ -10,14 +10,18 @@ A GFF interval, including attributes. If file is strictly a GFF file, only attribute is 'group.' """ - def __init__( self, reader, fields, chrom_col, start_col, end_col, strand_col, \ - score_col, default_strand, fix_strand=False, raw_line='' ): + def __init__( self, reader, fields, chrom_col, feature_col, start_col, end_col, \ + strand_col, score_col, default_strand, fix_strand=False, raw_line='' ): GenomicInterval.__init__( self, reader, fields, chrom_col, start_col, end_col, strand_col, \ default_strand, fix_strand=fix_strand ) - # Handle score column. + # Handle feature, score column. + self.feature_col = feature_col + if self.feature_col >= self.nfields: + raise MissingFieldError( "No field for feature_col (%d)" % feature_col ) + self.feature = self.fields[ self.feature_col ] self.score_col = score_col if self.score_col >= self.nfields: - raise MissingFieldError( "No field for score_col (%d)" % score_col ) + raise MissingFieldError( "No field for score_col (%d)" % score_col ) self.score = self.fields[ self.score_col ] # Attributes specific to GFF. @@ -28,10 +32,11 @@ """ A GFF feature, which can include multiple intervals. """ - def __init__( self, reader, chrom_col, start_col, end_col, strand_col, score_col, default_strand, \ - fix_strand=False, intervals=[] ): - GFFInterval.__init__( self, reader, intervals[0].fields, chrom_col, start_col, end_col, \ - strand_col, score_col, default_strand, fix_strand=fix_strand ) + def __init__( self, reader, chrom_col, feature_col, start_col, end_col, \ + strand_col, score_col, default_strand, fix_strand=False, intervals=[] ): + GFFInterval.__init__( self, reader, intervals[0].fields, chrom_col, feature_col, \ + start_col, end_col, strand_col, score_col, default_strand, \ + fix_strand=fix_strand ) self.intervals = intervals # Use intervals to set feature attributes. for interval in self.intervals: @@ -99,20 +104,20 @@ expect traditional interval format. """ - def __init__( self, reader, chrom_col=0, start_col=3, end_col=4, strand_col=6, score_col=5, \ - fix_strand=False, **kwargs ): + def __init__( self, reader, chrom_col=0, feature_col=2, start_col=3, \ + end_col=4, strand_col=6, score_col=5, fix_strand=False, **kwargs ): NiceReaderWrapper.__init__( self, reader, chrom_col=chrom_col, start_col=start_col, end_col=end_col, \ strand_col=strand_col, fix_strand=fix_strand, **kwargs ) - # HACK: NiceReaderWrapper (bx-python) does not handle score_col yet, so store ourselves. + self.feature_col = feature_col self.score_col = score_col self.last_line = None self.cur_offset = 0 self.seed_interval = None def parse_row( self, line ): - interval = GFFInterval( self, line.split( "\t" ), self.chrom_col, self.start_col, \ - self.end_col, self.strand_col, self.score_col, self.default_strand, \ - fix_strand=self.fix_strand, raw_line=line ) + interval = GFFInterval( self, line.split( "\t" ), self.chrom_col, self.feature_col, \ + self.start_col, self.end_col, self.strand_col, self.score_col, \ + self.default_strand, fix_strand=self.fix_strand, raw_line=line ) return interval def next( self ): @@ -196,8 +201,9 @@ self.seed_interval = interval # Return GFF feature with all intervals. - return GFFFeature( self, self.chrom_col, self.start_col, self.end_col, self.strand_col, \ - self.score_col, self.default_strand, fix_strand=self.fix_strand, \ + return GFFFeature( self, self.chrom_col, self.feature_col, self.start_col, \ + self.end_col, self.strand_col, self.score_col, \ + self.default_strand, fix_strand=self.fix_strand, \ intervals=feature_intervals ) --- a/tools/filters/gff/gff_filter_by_feature_count.py Tue Mar 08 16:17:09 2011 -0500 +++ b/tools/filters/gff/gff_filter_by_feature_count.py Tue Mar 08 19:01:59 2011 -0500 @@ -7,7 +7,7 @@ """ import sys from galaxy import eggs -from galaxy.datatypes.util.gff_util import parse_gff_attributes +from galaxy.datatypes.util.gff_util import GFFReaderWrapper assert sys.version_info[:2] >= ( 2, 4 ) @@ -58,77 +58,25 @@ break # Do filtering. - kept_lines = 0 + kept_features = 0 skipped_lines = 0 first_skipped_line = 0 out = open( output_name, 'w' ) - i = 0 - cur_transcript_id = None - cur_transcript_lines = [] - cur_transcript_feature_counts = {} # Key is feature name, value is feature count. - for i, line in enumerate( file( input_name ) ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ): - try: - # GFF format: chrom, source, feature, chromStart, chromEnd, score, strand, attributes - elems = line.split( '\t' ) - feature = elems[2] - start = str( long( elems[3] ) - 1 ) - coords = [ long( start ), long( elems[4] ) ] - strand = elems[6] - attributes = parse_gff_attributes( elems[8] ) - t_id = attributes.get( "transcript_id", None ) - - if not t_id: - # No transcript id, so pass line to output. - out.write( line ) - kept_lines += 1 - continue - - # There is a transcript ID, so process line at transcript level. - if t_id == cur_transcript_id: - # Line is element of transcript; increment feature count. - if not feature in cur_transcript_feature_counts: - cur_transcript_feature_counts[feature] = 0 - cur_transcript_feature_counts[feature] += 1 - cur_transcript_lines.append( line ) - continue - - # - # Line is part of new transcript; filter previous transcript. - # - - # Filter/write previous transcript. - result = eval( '%s %s' % ( cur_transcript_feature_counts.get( feature_name, 0 ), condition ) ) - if cur_transcript_id and result: - # Transcript passes filter; write transcript line to file." - out.write( "\n".join( cur_transcript_lines ) + "\n" ) - kept_lines += len( cur_transcript_lines ) - - # Start new transcript. - cur_transcript_id = t_id - cur_transcript_feature_counts = {} - cur_transcript_feature_counts[feature] = 1 - cur_transcript_lines = [ line ] - except Exception, e: - print e - skipped_lines += 1 - if not first_skipped_line: - first_skipped_line = i + 1 - else: - skipped_lines += 1 - if not first_skipped_line: - first_skipped_line = i + 1 - - # Write last transcript. - if cur_transcript_id and eval( '%s %s' % ( cur_transcript_feature_counts[feature_name], condition ) ): - # Transcript passes filter; write transcript lints to file. - out.write( "\n".join( cur_transcript_lines ) + "\n" ) - kept_lines += len( cur_transcript_lines ) + for i, feature in enumerate( GFFReaderWrapper( open( input_name ), fix_strand=True ) ): + count = 0 + for interval in feature.intervals: + if interval.feature == feature_name: + count += 1 + if eval( '%s %s' % ( count, condition ) ): + # Keep feature. + for interval in feature.intervals: + out.write( "\t".join(interval.fields) + '\n' ) + kept_features += 1 # Clean up. out.close() - info_msg = "%i lines kept (%.2f%%) using condition %s. " % ( kept_lines, float(kept_lines)/i * 100.0, feature_name + condition ) + info_msg = "%i of %i features kept (%.2f%%) using condition %s. " % \ + ( kept_features, i, float(kept_features)/i * 100.0, feature_name + condition ) if skipped_lines > 0: info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." %( skipped_lines, first_skipped_line ) print info_msg Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kellyv: Update SRMA test files so that functional tests pass
by Bitbucket 08 Mar '11

08 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/575531ef4a53/ changeset: r5201:575531ef4a53 user: kellyv date: 2011-03-08 22:17:09 summary: Update SRMA test files so that functional tests pass affected #: 5 files (10.7 MB) Diff too large to display. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add the ability to move data library items within a data library or between data libraries.
by Bitbucket 08 Mar '11

08 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ed7b6180b925/ changeset: r5200:ed7b6180b925 user: greg date: 2011-03-08 21:50:19 summary: Add the ability to move data library items within a data library or between data libraries. affected #: 7 files (16.8 KB) --- a/lib/galaxy/model/__init__.py Tue Mar 08 14:35:26 2011 -0500 +++ b/lib/galaxy/model/__init__.py Tue Mar 08 15:50:19 2011 -0500 @@ -941,6 +941,28 @@ self.description = description self.synopsis = synopsis self.root_folder = root_folder + def get_active_folders( self, folder, folders=None ): + # TODO: should we make sure the library is not deleted? + def sort_by_attr( seq, attr ): + """ + Sort the sequence of objects by object's attribute + Arguments: + seq - the list or any sequence (including immutable one) of objects to sort. + attr - the name of attribute to sort by + """ + # Use the "Schwartzian transform" + # Create the auxiliary list of tuples where every i-th tuple has form + # (seq[i].attr, i, seq[i]) and sort it. The second item of tuple is needed not + # only to provide stable sorting, but mainly to eliminate comparison of objects + # (which can be expensive or prohibited) in case of equal attribute values. + intermed = map( None, map( getattr, seq, ( attr, ) * len( seq ) ), xrange( len( seq ) ), seq ) + intermed.sort() + return map( operator.getitem, intermed, ( -1, ) * len( intermed ) ) + if folders is None: + active_folders = [ folder ] + for active_folder in folder.active_folders: + active_folders.extend( self.get_active_folders( active_folder, folders ) ) + return sort_by_attr( active_folders, 'id' ) def get_info_association( self, restrict=False, inherited=False ): if self.info_association: if not inherited or self.info_association[0].inheritable: --- a/lib/galaxy/web/controllers/library_common.py Tue Mar 08 14:35:26 2011 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Tue Mar 08 15:50:19 2011 -0500 @@ -1539,16 +1539,6 @@ show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) action = params.get( 'do_action', None ) - if action == 'import_to_histories': - return trans.response.send_redirect( web.url_for( controller='library_common', - action='import_datasets_to_histories', - cntrller=cntrller, - library_id=library_id, - ldda_ids=ldda_ids, - use_panels=use_panels, - show_deleted=show_deleted, - message=message, - status=status ) ) lddas = [] error = False is_admin = trans.user_is_admin() and cntrller == 'library_admin' @@ -1560,6 +1550,31 @@ error = True message = 'You must select an action to perform on the selected datasets.' else: + if action == 'import_to_histories': + return trans.response.send_redirect( web.url_for( controller='library_common', + action='import_datasets_to_histories', + cntrller=cntrller, + library_id=library_id, + ldda_ids=ldda_ids, + use_panels=use_panels, + show_deleted=show_deleted, + message=message, + status=status ) ) + if action == 'move': + if library_id in [ 'none', 'None', None ]: + source_library_id = '' + else: + source_library_id = library_id + return trans.response.send_redirect( web.url_for( controller='library_common', + action='move_library_item', + cntrller=cntrller, + source_library_id=source_library_id, + item_type='ldda', + item_id=ldda_ids, + use_panels=use_panels, + show_deleted=show_deleted, + message=message, + status=status ) ) ldda_ids = util.listify( ldda_ids ) for ldda_id in ldda_ids: try: @@ -1779,9 +1794,11 @@ @web.expose def import_datasets_to_histories( self, trans, cntrller, library_id='', folder_id='', ldda_ids='', target_history_ids='', new_history_name='', **kwd ): # This method is called from one of the following places: - # - a menu option for a library dataset ( ldda_ids will be a singel dataset id ) - # - a menu option for a library folder ( folder_id will have a value ) - # - a menu option for a library dataset search result set ( ldda_ids will be a comma separated string of dataset ids ) + # - a menu option for a library dataset ( ldda_ids is a single ldda id ) + # - a menu option for a library folder ( folder_id has a value ) + # - a select list option for acting on multiple selected datasets within a library + # ( ldda_ids is a comma separated string of ldda ids ) + # - a menu option for a library dataset search result set ( ldda_ids is a comma separated string of ldda ids ) params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -1799,13 +1816,7 @@ folder = None ldda_ids = util.listify( ldda_ids ) if ldda_ids: - # Check boxes cause 2 copies of each id to be included in the request ldda_ids = map( trans.security.decode_id, ldda_ids ) - unique_ldda_ids = [] - for ldda_id in ldda_ids: - if ldda_id not in unique_ldda_ids: - unique_ldda_ids.append( ldda_id ) - ldda_ids = unique_ldda_ids target_history_ids = util.listify( target_history_ids ) if target_history_ids: target_history_ids = [ trans.security.decode_id( target_history_id ) for target_history_id in target_history_ids if target_history_id ] @@ -1831,15 +1842,15 @@ status = 'error' for ldda in map( trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get, ldda_ids ): if ldda is None: - message += "You tried to import a library dataset that does not exist. " + message += "You tried to import a dataset that does not exist. " status = 'error' invalid_datasets += 1 elif ldda.dataset.state not in [ trans.model.Dataset.states.OK, trans.model.Dataset.states.ERROR ]: - message += "Cannot import dataset '%s' since its state is '%s'. " % ( ldda.name, ldda.dataset.state ) + message += "You cannot import dataset '%s' since its state is '%s'. " % ( ldda.name, ldda.dataset.state ) status = 'error' invalid_datasets += 1 elif not ldda.has_data(): - message += "Cannot import empty dataset '%s'. " % ldda.name + message += "You cannot import empty dataset '%s'. " % ldda.name status = 'error' invalid_datasets += 1 else: @@ -1931,6 +1942,226 @@ message=util.sanitize_text( message ), status='done' ) ) @web.expose + def move_library_item( self, trans, cntrller, item_type, item_id, source_library_id='', make_target_current=True, **kwd ): + # This method is called from one of the following places: + # - a menu option for a library dataset ( item_type is 'ldda' and item_id is a single ldda id ) + # - a menu option for a library folder ( item_type is 'folder' and item_id is a single folder id ) + # - a select list option for acting on multiple selected datasets within a library ( item_type is + # 'ldda' and item_id is a comma separated string of ldda ids ) + # - a menu option for a library dataset search result set ( item_type is 'ldda' and item_id is a + # comma separated string of ldda ids ) + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) + make_target_current = util.string_as_bool( make_target_current ) + is_admin = trans.user_is_admin() and cntrller == 'library_admin' + user = trans.get_user() + current_user_roles = trans.get_current_user_roles() + move_ldda_ids = [] + move_lddas = [] + move_folder_id = [] + move_folder = None + if source_library_id: + source_library = trans.sa_session.query( trans.model.Library ).get( trans.security.decode_id( source_library_id ) ) + else: + # Request sent from the library_dataset_search_results page. + source_library = None + target_library_id = params.get( 'target_library_id', '' ) + if target_library_id not in [ '', 'none', None ]: + target_library = trans.sa_session.query( trans.model.Library ).get( trans.security.decode_id( target_library_id ) ) + elif make_target_current: + target_library = source_library + else: + target_library = None + target_folder_id = params.get( 'target_folder_id', '' ) + if target_folder_id not in [ '', 'none', None ]: + target_folder = trans.sa_session.query( trans.model.LibraryFolder ).get( trans.security.decode_id( target_folder_id ) ) + if target_library is None: + target_library = target_folder.parent_library + else: + target_folder = None + if item_type == 'ldda': + # We've been called from a menu option for a library dataset search result set + move_ldda_ids = util.listify( item_id ) + if move_ldda_ids: + # Checkboxes cause 2 copies of each id to be included in the request + move_ldda_ids = map( trans.security.decode_id, move_ldda_ids ) + unique_ldda_ids = [] + for ldda_id in move_ldda_ids: + if ldda_id not in unique_ldda_ids: + unique_ldda_ids.append( ldda_id ) + move_ldda_ids = unique_ldda_ids + elif item_type == 'folder': + move_folder_id = item_id + move_folder = trans.sa_session.query( trans.model.LibraryFolder ).get( trans.security.decode_id( move_folder_id ) ) + if params.get( 'move_library_item_button', False ): + if not ( move_ldda_ids or move_folder_id ) or target_folder_id in [ '', 'none', None ]: + message = "You must select a source folder or one or more source datasets, and a target folder." + status = 'error' + else: + valid_lddas = [] + invalid_lddas = [] + invalid_items = 0 + flush_required = False + if item_type == 'ldda': + for ldda in map( trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get, move_ldda_ids ): + if ldda is None: + message += "You tried to move a dataset that does not exist. " + status = 'error' + invalid_items += 1 + elif ldda.dataset.state not in [ trans.model.Dataset.states.OK, trans.model.Dataset.states.ERROR ]: + message += "You cannot move dataset '%s' since its state is '%s'. " % ( ldda.name, ldda.dataset.state ) + status = 'error' + invalid_items += 1 + elif not ldda.has_data(): + message += "You cannot move empty dataset '%s'. " % ldda.name + status = 'error' + invalid_items += 1 + else: + if is_admin: + library_dataset = ldda.library_dataset + library_dataset.folder = target_folder + trans.sa_session.add( library_dataset ) + flush_required = True + else: + if trans.app.security_agent.can_modify_library_item( current_user_roles, ldda ): + valid_lddas.append( ldda ) + library_dataset = ldda.library_dataset + library_dataset.folder = target_folder + trans.sa_session.add( library_dataset ) + flush_required = True + else: + invalid_items += 1 + invalid_lddas.append( ldda ) + if not valid_lddas: + message = "You are not authorized to move any of the selected datasets." + elif invalid_lddas: + message += "You are not authorized to move %s: " % inflector.cond_plural( len( invalid_lddas ), "dataset" ) + for ldda in invalid_lddas: + message += '(%s)' % ldda.name + message += '. ' + num_source = len( move_ldda_ids ) - invalid_items + message = "%i %s moved to folder (%s) within data library (%s)" % ( num_source, + inflector.cond_plural( num_source, "dataset" ), + target_folder.name, + target_library.name ) + elif item_type == 'folder': + move_folder = trans.sa_session.query( trans.app.model.LibraryFolder ) \ + .get( trans.security.decode_id( move_folder_id ) ) + if move_folder is None: + message += "You tried to move a folder that does not exist. " + status = 'error' + invalid_items += 1 + else: + move_folder.parent = target_folder + trans.sa_session.add( move_folder ) + flush_required = True + message = "Moved folder (%s) to folder (%s) within data library (%s) " % ( move_folder.name, + target_folder.name, + target_library.name ) + if flush_required: + trans.sa_session.flush() + if target_library: + if is_admin: + target_library_folders = target_library.get_active_folders( target_library.root_folder ) + else: + folders_with_permission_to_add = [] + for folder in target_library.get_active_folders( target_library.root_folder ): + if trans.app.security_agent.can_add_library_item( current_user_roles, folder ): + folders_with_permission_to_add.append( folder ) + target_library_folders = folders_with_permission_to_add + else: + target_library_folders = [] + if item_type == 'ldda': + for ldda_id in move_ldda_ids: + # TODO: It is difficult to filter out undesired folders (e.g. the ldda's current + # folder) if we have a list of lddas, but we may want to filter folders that + # are easily handled. + ldda = trans.sa_session.query( trans.model.LibraryDatasetDatasetAssociation ).get( ldda_id ) + move_lddas.append( ldda ) + elif item_type == 'folder': + def __is_contained_in( folder1, folder2 ): + # Return True if folder1 is contained in folder2 + if folder1.parent: + if folder1.parent == folder2: + return True + return __is_contained_in( folder1.parent, folder2 ) + return False + filtered_folders = [] + for folder in target_library_folders: + include = True + if move_folder: + if __is_contained_in( folder, move_folder ): + # Don't allow moving a folder to one of it's sub-folders (circular issues in db) + include = False + if move_folder.id == folder.id: + # Don't allow moving a folder to itself + include = False + if move_folder.parent and move_folder.parent.id == folder.id: + # Don't allow moving a folder to it's current parent folder + include = False + if include: + filtered_folders.append( folder ) + target_library_folders = filtered_folders + def __build_target_library_id_select_field( trans, selected_value='none' ): + # Get all the libraries for which the current user can add items. + target_libraries = [] + if is_admin: + for library in trans.sa_session.query( trans.model.Library ) \ + .filter( trans.model.Library.deleted == False ) \ + .order_by( trans.model.Library.table.c.name ): + if source_library is None or library.id != source_library.id: + target_libraries.append( library ) + else: + for library in trans.app.security_agent.get_accessible_libraries( trans, user ): + if source_library is None: + if trans.app.security_agent.can_add_library_item( current_user_roles, library ): + target_libraries.append( library ) + elif library.id != source_library.id: + if trans.app.security_agent.can_add_library_item( current_user_roles, library ): + target_libraries.append( library ) + # A refresh_on_change is required to display the selected library's folders + return build_select_field( trans, + objs=target_libraries, + label_attr='name', + select_field_name='target_library_id', + selected_value=selected_value, + refresh_on_change=True ) + def __build_target_folder_id_select_field( trans, folders, selected_value='none' ): + for folder in folders: + if not folder.parent: + folder.name = 'Data library root folder' + return build_select_field( trans, + objs=folders, + label_attr='name', + select_field_name='target_folder_id', + selected_value=selected_value, + refresh_on_change=False ) + if target_library: + selected_value = target_library.id + else: + selected_value = 'none' + target_library_id_select_field = __build_target_library_id_select_field( trans, selected_value=selected_value ) + target_folder_id_select_field = __build_target_folder_id_select_field( trans, target_library_folders ) + return trans.fill_template( "/library/common/move_library_item.mako", + cntrller=cntrller, + make_target_current=make_target_current, + source_library=source_library, + item_type=item_type, + item_id=item_id, + move_ldda_ids=move_ldda_ids, + move_lddas=move_lddas, + move_folder=move_folder, + target_library=target_library, + target_library_id_select_field=target_library_id_select_field, + target_folder_id_select_field=target_folder_id_select_field, + show_deleted=show_deleted, + use_panels=use_panels, + message=message, + status=status ) + @web.expose def delete_library_item( self, trans, cntrller, library_id, item_id, item_type, **kwd ): # This action will handle deleting all types of library items. State is saved for libraries and # folders ( i.e., if undeleted, the state of contents of the library or folder will remain, so previously @@ -2257,7 +2488,7 @@ # Perform search parser = MultifieldParser( [ 'name', 'info', 'dbkey', 'message' ], schema=schema ) # Search term with wildcards may be slow... - results = searcher.search( parser.parse( '*' + search_term + '*' ), minscore=0.5 ) + results = searcher.search( parser.parse( '*' + search_term + '*' ), minscore=0.01 ) ldda_ids = [ result[ 'id' ] for result in results ] lddas = [] for ldda_id in ldda_ids: --- a/templates/library/common/browse_library.mako Tue Mar 08 14:35:26 2011 -0500 +++ b/templates/library/common/browse_library.mako Tue Mar 08 15:50:19 2011 -0500 @@ -247,19 +247,20 @@ checked="checked" %endif /> - %if ldda.library_dataset.deleted: - <span class="libraryItem-error"> - %endif <div style="float: left; margin-left: 1px;" class="menubutton split popup" id="dataset-${ldda.id}-popup"> - <a class="view-info" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">${ldda.name}</a> + <a class="view-info" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}"> + %if ldda.library_dataset.deleted: + <div class="libraryItem-error">${ldda.name}</div> + %else: + ${ldda.name} + %endif + </a></div> - %if ldda.library_dataset.deleted: - </span> - %endif %if not library.deleted: <div popupmenu="dataset-${ldda.id}-popup"> %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify: <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='move_library_item', cntrller=cntrller, item_type='ldda', item_id=trans.security.encode_id( ldda.id ), source_library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Move this dataset</a> %else: <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> %endif @@ -348,7 +349,7 @@ info_association, inherited = folder.get_info_association( restrict=True ) %> %if not root_folder and ( not folder.deleted or show_deleted ): - <% encoded_id = trans.security.encode_id(folder.id) %> + <% encoded_id = trans.security.encode_id( folder.id ) %><tr id="folder-${encoded_id}" class="folderRow libraryOrFolderRow" %if parent is not None: parent="${parent}" @@ -358,15 +359,16 @@ <td style="padding-left: ${folder_pad}px;"><input type="checkbox" class="folderCheckbox"/><span class="expandLink folder-${encoded_id}-click"> - <div style="float: left; margin-left: 2px;" class="menubutton split popup" id="folder_img-${folder.id}-popup"> - <a class="folder-${encoded_id}-click" href="javascript:void(0);"> - %if folder.deleted: - <span class="libraryItem-error">${folder.name}</span> - %else: - ${folder.name} - %endif - </a> - </div> + <div style="float: left; margin-left: 2px;" class="menubutton split popup" id="folder_img-${folder.id}-popup"> + <a class="folder-${encoded_id}-click" href="javascript:void(0);"> + %if folder.deleted: + <div class="libraryItem-error">${folder.name}</div> + %else: + ${folder.name} + %endif + </a> + </div> + </span> %if not library.deleted: <div popupmenu="folder_img-${folder.id}-popup"> %if not branch_deleted( folder ) and can_add: @@ -379,6 +381,7 @@ %endif %if can_modify: <a class="action-button" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='move_library_item', cntrller=cntrller, item_type='folder', item_id=trans.security.encode_id( folder.id ), source_library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Move this folder</a> %else: <a class="action-button" class="view-info" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> %endif --- a/templates/library/common/common.mako Tue Mar 08 14:35:26 2011 -0500 +++ b/templates/library/common/common.mako Tue Mar 08 15:50:19 2011 -0500 @@ -399,17 +399,18 @@ can_download = 'download' not in actions_to_exclude can_import_to_histories = 'import_to_histories' not in actions_to_exclude can_manage_permissions = 'manage_permissions' not in actions_to_exclude + can_move = 'move' not in actions_to_exclude %><tfoot><tr><td colspan="5" style="padding-left: 42px;"> - For selected items: + For selected datasets: <select name="do_action" id="action_on_selected_items"> %if can_import_to_histories: %if not is_admin and default_action == 'import_to_histories': - <option value="import_to_histories" selected>Import selected datasets to histories</option> + <option value="import_to_histories" selected>Import to histories</option> %else: - <option value="import_to_histories">Import selected datasets to histories</option> + <option value="import_to_histories">Import to histories</option> %endif %endif %if can_manage_permissions: @@ -419,13 +420,19 @@ <option value="manage_permissions">Edit permissions</option> %endif %endif + %if can_move: + <option value="move">Move</option> + %endif + %if can_delete: + <option value="delete">Delete</option> + %endif %if can_download: %if 'gz' in comptypes: <option value="tgz" %if default_action == 'download': selected %endif> - >Download as a .tar.gz file</option> + >Download as a .tar.gz file</option> %endif %if 'bz2' in comptypes: <option value="tbz">Download as a .tar.bz2 file</option> @@ -442,9 +449,6 @@ >Download as a .zip file</option> %endif %endif - %if can_delete: - <option value="delete">Delete</option> - %endif </select><input type="submit" class="primary-button" name="action_on_datasets_button" id="action_on_datasets_button" value="Go"/></td> --- a/templates/library/common/import_datasets_to_histories.mako Tue Mar 08 14:35:26 2011 -0500 +++ b/templates/library/common/import_datasets_to_histories.mako Tue Mar 08 15:50:19 2011 -0500 @@ -4,74 +4,53 @@ <%def name="title()">Import library datasets to histories</%def><%def name="javascripts()"> - -${parent.javascripts()} -${h.js( "jquery", "galaxy.base" )} -<script type="text/javascript"> - $(function() { - $("#select-multiple").click(function() { - $("#single-dest-select").val(""); - $("#single-destination").hide(); - $("#multiple-destination").show(); + ${parent.javascripts()} + ${h.js( "jquery", "galaxy.base" )} + <script type="text/javascript"> + $(function() { + $("#select-multiple").click(function() { + $("#single-dest-select").val(""); + $("#single-destination").hide(); + $("#multiple-destination").show(); + }); }); - }); -</script> - + </script></%def> %if message: ${render_msg( message, status )} %endif -<p> - <div class="infomessage">Import library datasets into histories.</div> - <div style="clear: both"></div> -</p> -<p> - <form method="post"> - <div class="toolForm" style="float: left; width: 45%; padding: 0px;"> - <div class="toolFormBody"> - <input type="hidden" name="cntrller" value="${cntrller}"/> - %if source_lddas: - %for source_ldda in source_lddas: - <% - checked = "" - encoded_id = trans.security.encode_id( source_ldda.id ) - if source_ldda.id in ldda_ids: - checked = " checked='checked'" - %> - <div class="form-row"> - <input type="checkbox" name="ldda_ids" id="dataset_${encoded_id}" value="${encoded_id}" ${checked}/> - <label for="dataset_${encoded_id}" style="display: inline;font-weight:normal;">${source_ldda.name}</label> - </div> - %endfor - %else: - <div class="form-row">This folder has no accessible library datasets.</div> - %endif - </div> +<b>Import library datasets into histories</b> +<br/><br/> +<form action="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, use_panels=use_panels, show_deleted=show_deleted )}" method="post"> + <div class="toolForm" style="float: left; width: 45%; padding: 0px;"> + <div class="toolFormBody"> + %if source_lddas: + %for source_ldda in source_lddas: + <% + checked = "" + encoded_id = trans.security.encode_id( source_ldda.id ) + if source_ldda.id in ldda_ids: + checked = " checked='checked'" + %> + <div class="form-row"> + <input type="checkbox" name="ldda_ids" id="dataset_${encoded_id}" value="${encoded_id}" ${checked}/> + <label for="dataset_${encoded_id}" style="display: inline;font-weight:normal;">${source_ldda.name}</label> + </div> + %endfor + %else: + <div class="form-row">This folder has no accessible library datasets.</div> + %endif </div> - <div style="float: left; padding-left: 10px; font-size: 36px;">→</div> - <div class="toolForm" style="float: right; width: 45%; padding: 0px;"> - <div class="toolFormTitle">Destination Histories:</div> - <div class="toolFormBody"> - <div class="form-row" id="single-destination"> - <select id="single-dest-select" name="target_history_ids"> - <option value=""></option> - %for i, target_history in enumerate( target_histories ): - <% - encoded_id = trans.security.encode_id( target_history.id ) - if target_history == current_history: - current_history_text = " (current history)" - else: - current_history_text = "" - %> - <option value="${encoded_id}">${i + 1}: ${h.truncate( target_history.name, 30 )}${current_history_text}</option> - %endfor - </select> - <br/><br/> - <a style="margin-left: 10px;" href="javascript:void(0);" id="select-multiple">Choose multiple histories</a> - </div> - <div id="multiple-destination" style="display: none;"> + </div> + <div style="float: left; padding-left: 10px; font-size: 36px;">→</div> + <div class="toolForm" style="float: right; width: 45%; padding: 0px;"> + <div class="toolFormTitle">Destination Histories:</div> + <div class="toolFormBody"> + <div class="form-row" id="single-destination"> + <select id="single-dest-select" name="target_history_ids"> + <option value=""></option> %for i, target_history in enumerate( target_histories ): <% encoded_id = trans.security.encode_id( target_history.id ) @@ -80,31 +59,45 @@ else: current_history_text = "" %> - <div class="form-row"> - <input type="checkbox" name="target_history_ids" id="target_history_${encoded_id}" value="${encoded_id}"/> - <label for="target_history_${encoded_id}" style="display: inline; font-weight:normal;">${i + 1}: ${target_history.name}${current_history_text}</label> - </div> + <option value="${encoded_id}">${i + 1}: ${h.truncate( target_history.name, 30 )}${current_history_text}</option> %endfor + </select> + <br/><br/> + <a style="margin-left: 10px;" href="javascript:void(0);" id="select-multiple">Choose multiple histories</a> + </div> + <div id="multiple-destination" style="display: none;"> + %for i, target_history in enumerate( target_histories ): + <% + encoded_id = trans.security.encode_id( target_history.id ) + if target_history == current_history: + current_history_text = " (current history)" + else: + current_history_text = "" + %> + <div class="form-row"> + <input type="checkbox" name="target_history_ids" id="target_history_${encoded_id}" value="${encoded_id}"/> + <label for="target_history_${encoded_id}" style="display: inline; font-weight:normal;">${i + 1}: ${target_history.name}${current_history_text}</label> + </div> + %endfor + </div> + %if trans.get_user(): + <% + checked = "" + if "create_new_history" in target_history_ids: + checked = " checked='checked'" + %> + <hr /> + <div style="text-align: center; color: #888;">— OR —</div> + <div class="form-row"> + <label for="new_history_name" style="display: inline; font-weight:normal;">New history named:</label> + <input type="textbox" name="new_history_name" /></div> - %if trans.get_user(): - <% - checked = "" - if "create_new_history" in target_history_ids: - checked = " checked='checked'" - %> - <hr /> - <div style="text-align: center; color: #888;">— OR —</div> - <div class="form-row"> - <label for="new_history_name" style="display: inline; font-weight:normal;">New history named:</label> - <input type="textbox" name="new_history_name" /> - </div> - %endif - </div> + %endif </div> - <div style="clear: both"></div> - <div class="form-row" align="center"> - <input type="submit" class="primary-button" name="import_datasets_to_histories_button" value="Import library datasets"/> - </div> - </form></div> -</p> + <div style="clear: both"></div> + <div class="form-row" align="center"> + <input type="submit" class="primary-button" name="import_datasets_to_histories_button" value="Import library datasets"/> + </div> + </form> +</div> --- a/templates/library/common/library_dataset_search_results.mako Tue Mar 08 14:35:26 2011 -0500 +++ b/templates/library/common/library_dataset_search_results.mako Tue Mar 08 15:50:19 2011 -0500 @@ -95,7 +95,7 @@ <p>The string "${search_term}" was found in at least one of the following information components of the displayed library datasets.</p> ${render_searched_components()} <form name="act_on_multiple_datasets" action="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, use_panels=use_panels, show_deleted=show_deleted )}" onSubmit="javascript:return checkForm();" method="post"> - <input type="hidden" name=search_term value="${search_term}"/> + <input type="hidden" name="search_term" value="${search_term}"/><table cellspacing="0" cellpadding="0" border="0" width="100%" class="grid" id="library-grid"><thead><tr class="libraryTitle"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: rc: Add import statement for binascii
by Bitbucket 08 Mar '11

08 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6f03367736a8/ changeset: r5199:6f03367736a8 user: rc date: 2011-03-08 20:35:26 summary: Add import statement for binascii affected #: 1 file (16 bytes) --- a/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py Tue Mar 08 14:08:07 2011 -0500 +++ b/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py Tue Mar 08 14:35:26 2011 -0500 @@ -7,6 +7,7 @@ from migrate import * from migrate.changeset import * from sqlalchemy.exc import * +import binascii from galaxy.util.json import from_json_string, to_json_string Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: rc: Added the postgres9 json sniffnfix method to the migration script instead of importing it from custom_types.py
by Bitbucket 08 Mar '11

08 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e844d6edf929/ changeset: r5198:e844d6edf929 user: rc date: 2011-03-08 20:08:07 summary: Added the postgres9 json sniffnfix method to the migration script instead of importing it from custom_types.py affected #: 1 file (319 bytes) --- a/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py Tue Mar 08 12:42:26 2011 -0500 +++ b/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py Tue Mar 08 14:08:07 2011 -0500 @@ -9,7 +9,6 @@ from sqlalchemy.exc import * from galaxy.util.json import from_json_string, to_json_string -from galaxy.model.custom_types import _sniffnfix_pg9_hex import logging log = logging.getLogger( __name__ ) @@ -17,6 +16,18 @@ metadata = MetaData( migrate_engine ) db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) +def _sniffnfix_pg9_hex(value): + """ + Sniff for and fix postgres 9 hex decoding issue + + """ + try: + if value[0] == 'x': + return binascii.unhexlify(value[1:]) + else: + return value + except Exception, ex: + return value def upgrade(): print __doc__ @@ -32,7 +43,7 @@ # first check if loading the dict from the json succeeds # if that fails, it means that the content field is corrupted. try: - field_values_dict = from_json_string( str( row['field_values'] ) ) + field_values_dict = from_json_string( _sniffnfix_pg9_hex( str( row['field_values'] ) ) ) except Exception, e: corrupted_rows = corrupted_rows + 1 # content field is corrupted @@ -72,7 +83,10 @@ json_values = to_json_string(field_values_dict) cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( json_values, int( row['id'] ) ) db_session.execute( cmd ) - print 'Fixed %i corrupted rows.' % corrupted_rows + if corrupted_rows: + print 'Fixed %i corrupted rows.' % corrupted_rows + else: + print 'No corrupted rows found.' def downgrade(): pass \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: rc: Fixes the data corruption caused in the form_values table (content field) by the migrate script 65.
by Bitbucket 08 Mar '11

08 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0ce107ca4e8b/ changeset: r5197:0ce107ca4e8b user: rc date: 2011-03-08 18:42:26 summary: Fixes the data corruption caused in the form_values table (content field) by the migrate script 65. affected #: 1 file (0 bytes) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: An uninitialized value in R's PDF driver was causing it to sometimes randomly add a few elements to PDF outputs. The bug has been fixed in the buildbot environment and these changes account for that fix.
by Bitbucket 08 Mar '11

08 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/86b7fa44549c/ changeset: r5196:86b7fa44549c user: natefoo date: 2011-03-08 17:17:57 summary: An uninitialized value in R's PDF driver was causing it to sometimes randomly add a few elements to PDF outputs. The bug has been fixed in the buildbot environment and these changes account for that fix. affected #: 17 files (728 bytes) --- a/test-data/peakcalling_macs/test2/Galaxy_Test_Run_model.pdf Tue Mar 08 10:26:52 2011 -0500 +++ b/test-data/peakcalling_macs/test2/Galaxy_Test_Run_model.pdf Tue Mar 08 11:17:57 2011 -0500 @@ -28,7 +28,7 @@ \/Length\ 7\ 0\ R \>\> stream -q +[1Jj ]*q Q\ q\ 59\.04\ 73\.44\ 342\.72\ 299\.52\ re\ W\ n 1\.000\ 0\.000\ 0\.000\ RG 0\.75\ w @@ -3759,7 +3759,7 @@ endstream endobj 7\ 0\ obj -59450 +5945[0-9] endobj 3\ 0\ obj \<\< --- a/test/base/twilltestcase.py Tue Mar 08 10:26:52 2011 -0500 +++ b/test/base/twilltestcase.py Tue Mar 08 11:17:57 2011 -0500 @@ -75,7 +75,7 @@ # PDF files contain creation dates, modification dates, ids and descriptions that change with each # new file, so we need to handle these differences. As long as the rest of the PDF file does # not differ we're ok. - valid_diff_strs = [ 'description', 'createdate', 'creationdate', 'moddate', 'id', 'producer', 'creator', 'extgstate', 'ais' ] + valid_diff_strs = [ 'description', 'createdate', 'creationdate', 'moddate', 'id', 'producer', 'creator' ] valid_diff = False invalid_diff_lines = 0 for line in diff_slice: --- a/tools/multivariate_stats/cca.xml Tue Mar 08 10:26:52 2011 -0500 +++ b/tools/multivariate_stats/cca.xml Tue Mar 08 11:17:57 2011 -0500 @@ -52,7 +52,7 @@ <param name="y_scale" value="scale"/><param name="std_scores" value="yes"/><output name="out_file1" file="cca_out1.tabular"/> - <output name="out_file2" file="cca_out2.pdf" lines_diff="6"/> + <output name="out_file2" file="cca_out2.pdf"/></test></tests><help> --- a/tools/multivariate_stats/kpca.xml Tue Mar 08 10:26:52 2011 -0500 +++ b/tools/multivariate_stats/kpca.xml Tue Mar 08 11:17:57 2011 -0500 @@ -108,7 +108,7 @@ <param name="scale" value="1"/><param name="degree" value="2"/><output name="out_file1" file="kpca_out1.tabular"/> - <output name="out_file2" file="kpca_out2.pdf" lines_diff="6"/> + <output name="out_file2" file="kpca_out2.pdf"/></test></tests><help> --- a/tools/multivariate_stats/pca.xml Tue Mar 08 10:26:52 2011 -0500 +++ b/tools/multivariate_stats/pca.xml Tue Mar 08 11:17:57 2011 -0500 @@ -47,14 +47,14 @@ <param name="var_cols" value="1,2,3,4"/><param name="method" value="cor"/><output name="out_file1" file="pca_out1.tabular"/> - <output name="out_file2" file="pca_out2.pdf" lines_diff="6"/> + <output name="out_file2" file="pca_out2.pdf"/></test><test><param name="input1" value="iris.tabular"/><param name="var_cols" value="1,2,3,4"/><param name="method" value="cov"/><output name="out_file1" file="pca_out3.tabular"/> - <output name="out_file2" file="pca_out4.pdf" lines_diff="6"/> + <output name="out_file2" file="pca_out4.pdf"/></test><test><param name="input1" value="iris.tabular"/> @@ -62,7 +62,7 @@ <param name="method" value="svd"/><param name="scale" value="both"/><output name="out_file1" file="pca_out5.tabular"/> - <output name="out_file2" file="pca_out6.pdf" lines_diff="6"/> + <output name="out_file2" file="pca_out6.pdf"/></test></tests><help> --- a/tools/plotting/histogram2.xml Tue Mar 08 10:26:52 2011 -0500 +++ b/tools/plotting/histogram2.xml Tue Mar 08 11:17:57 2011 -0500 @@ -22,7 +22,7 @@ <param name="xlab" value="V1"/><param name="density" value="true"/><param name="frequency" value="false"/> - <output name="out_file1" file="histogram_out1.pdf" lines_diff="6" /> + <output name="out_file1" file="histogram_out1.pdf"/></test></tests><requirements> --- a/tools/regVariation/draw_stacked_barplots.xml Tue Mar 08 10:26:52 2011 -0500 +++ b/tools/regVariation/draw_stacked_barplots.xml Tue Mar 08 11:17:57 2011 -0500 @@ -16,7 +16,7 @@ <tests><test><param name="inputFile1" value="categories_criteria.tabular" /> - <output name="outputFile1" file="statcked_bars_plot.pdf" /> + <output name="outputFile1" file="stacked_barplot.pdf" /></test></tests> --- a/tools/regVariation/linear_regression.xml Tue Mar 08 10:26:52 2011 -0500 +++ b/tools/regVariation/linear_regression.xml Tue Mar 08 11:17:57 2011 -0500 @@ -29,7 +29,7 @@ <param name="response_col" value="3"/><param name="predictor_cols" value="1,2"/><output name="out_file1" file="regr_out.tabular"/> - <output name="out_file2" file="regr_out.pdf" lines_diff="6"/> + <output name="out_file2" file="regr_out.pdf"/></test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Remove debugging statement.
by Bitbucket 08 Mar '11

08 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/58f118c440ad/ changeset: r5195:58f118c440ad user: jgoecks date: 2011-03-08 16:26:52 summary: Remove debugging statement. affected #: 1 file (83 bytes) --- a/static/scripts/trackster.js Tue Mar 08 10:04:39 2011 -0500 +++ b/static/scripts/trackster.js Tue Mar 08 10:26:52 2011 -0500 @@ -1573,7 +1573,6 @@ if (clear_after) { var track = this; var intervalId = setInterval(function() { - console.log("draw_tile_dict_length:", obj_length(draw_tile_dict)); if (obj_length(draw_tile_dict) === 0) { // All tiles have been drawn; clear out track content in order to show the most recent content. // Most recent content is the div with children (tiles) most recently appended to track. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0