April 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dannon: Fix zipfile failure for composite datatypes. Rename variables in data.display method to be consistent with 'data' for hda naming convention. Remove duplicated comment from tabular_chunked.mako.
by Bitbucket 18 Apr '12

18 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bb1d639c4db5/ changeset: bb1d639c4db5 user: dannon date: 2012-04-19 00:49:31 summary: Fix zipfile failure for composite datatypes. Rename variables in data.display method to be consistent with 'data' for hda naming convention. Remove duplicated comment from tabular_chunked.mako. affected #: 2 files diff -r 80014059ed11eee51551b143d56780be2d234068 -r bb1d639c4db59c50f7384c8b2ef22a7b8da896ee lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -5,10 +5,37 @@ from galaxy.util import inflector from galaxy.util.sanitize_html import sanitize_html from cgi import escape +import mimetypes import metadata import zipfile from metadata import MetadataElement #import directly to maintain ease of use in Datatype class definitions + +if sys.version_info[:2] < ( 2, 6 ): + zipfile.BadZipFile = zipfile.error +if sys.version_info[:2] < ( 2, 5 ): + zipfile.LargeZipFile = zipfile.error + +tmpd = tempfile.mkdtemp() +comptypes=[] +ziptype = '32' +tmpf = os.path.join( tmpd, 'compression_test.zip' ) +try: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) + archive.close() + comptypes.append( 'zip' ) + ziptype = '64' +except RuntimeError: + log.exception( "Compression error when testing zip compression. This option will be disabled for library downloads." ) +except (TypeError, zipfile.LargeZipFile): # ZIP64 is only in Python2.5+. Remove TypeError when 2.4 support is dropped + log.warning( 'Max zip file size is 2GB, ZIP64 not supported' ) + comptypes.append( 'zip' ) +try: + os.unlink( tmpf ) +except OSError: + pass +os.rmdir( tmpd ) + log = logging.getLogger(__name__) # Valid first column and strand column values vor bed, other formats @@ -256,16 +283,16 @@ trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (dataset.hid, fname, to_ext) return open( dataset.file_name ) - def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, size=None, offset=None, **kwd): + def display_data(self, trans, data, preview=False, filename=None, to_ext=None, size=None, offset=None, **kwd): """ Old display method, for transition """ #Relocate all composite datatype display to a common location. composite_extensions = trans.app.datatypes_registry.get_composite_extensions( ) composite_extensions.append('html') # for archiving composite datatypes - if isinstance( dataset, basestring ): - return dataset + if isinstance( data, basestring ): + return data if filename and filename != "index": # For files in extra_files_path - file_path = trans.app.object_store.get_filename(dataset, extra_dir='dataset_%s_files' % dataset.id, alt_name=filename) + file_path = trans.app.object_store.get_filename(data.dataset, extra_dir='dataset_%s_files' % data.dataset.id, alt_name=filename) if os.path.exists( file_path ): if os.path.isdir( file_path ): return trans.show_error_message( "Directory listing is not allowed." ) #TODO: Reconsider allowing listing of directories? @@ -279,43 +306,36 @@ return open( file_path ) else: return trans.show_error_message( "Could not find '%s' on the extra files path %s." % ( filename, file_path ) ) - trans.response.set_content_type(dataset.get_mime()) - trans.log_event( "Display dataset id: %s" % str( dataset.id ) ) + trans.response.set_content_type(data.get_mime()) + trans.log_event( "Display dataset id: %s" % str( data.id ) ) from galaxy import datatypes #DBTODO REMOVE THIS AT REFACTOR - if to_ext or isinstance(dataset.datatype, datatypes.binary.Binary): # Saving the file, or binary file - if dataset.extension in composite_extensions: - return self._archive_composite_dataset( trans, dataset, **kwd ) + if to_ext or isinstance(data.datatype, datatypes.binary.Binary): # Saving the file, or binary file + if data.extension in composite_extensions: + return self._archive_composite_dataset( trans, data, **kwd ) else: - trans.response.headers['Content-Length'] = int( os.stat( dataset.file_name ).st_size ) + trans.response.headers['Content-Length'] = int( os.stat( data.file_name ).st_size ) if not to_ext: - to_ext = dataset.extension + to_ext = data.extension valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - fname = ''.join(c in valid_chars and c or '_' for c in dataset.name)[0:150] + fname = ''.join(c in valid_chars and c or '_' for c in data.name)[0:150] trans.response.set_content_type( "application/octet-stream" ) #force octet-stream so Safari doesn't append mime extensions to filename - trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (dataset.hid, fname, to_ext) - return open( dataset.file_name ) - if not os.path.exists( dataset.file_name ): - raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % dataset.file_name ) + trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (data.hid, fname, to_ext) + return open( data.file_name ) + if not os.path.exists( data.file_name ): + raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % data.file_name ) max_peek_size = 1000000 # 1 MB - if isinstance(dataset.datatype, datatypes.images.Html): + if isinstance(data.datatype, datatypes.images.Html): max_peek_size = 10000000 # 10 MB for html - if not preview or isinstance(dataset.datatype, datatypes.images.Image) or os.stat( dataset.file_name ).st_size < max_peek_size: + if not preview or isinstance(data.datatype, datatypes.images.Image) or os.stat( data.file_name ).st_size < max_peek_size: if trans.app.config.sanitize_all_html and trans.response.get_content_type() == "text/html": # Sanitize anytime we respond with plain text/html content. - return sanitize_html(open( dataset.file_name ).read()) - return open( dataset.file_name ) + return sanitize_html(open( data.file_name ).read()) + return open( data.file_name ) else: trans.response.set_content_type( "text/html" ) return trans.stream_template_mako( "/dataset/large_file.mako", - truncated_data = open( dataset.file_name ).read(max_peek_size), - data = dataset ) - """Returns dataset contents for display. - This allows for customization of subtype displays""" - file_path = trans.app.object_store.get_filename(dataset, extra_dir='dataset_%s_files' % dataset.id, alt_name=filename) - if size: - return open(dataset.file_path).read(size) - else: - open(dataset.file_path) + truncated_data = open( data.file_name ).read(max_peek_size), + data = data) def display_name(self, dataset): """Returns formatted html of dataset name""" diff -r 80014059ed11eee51551b143d56780be2d234068 -r bb1d639c4db59c50f7384c8b2ef22a7b8da896ee templates/dataset/tabular_chunked.mako --- a/templates/dataset/tabular_chunked.mako +++ b/templates/dataset/tabular_chunked.mako @@ -50,7 +50,6 @@ row.append($('<td>')); } else{ - /* SAM file or like format with optional metadata missing */ /* Comment line, just return the one cell*/ row.append(renderCell(line, 0, DATASET_COLS)); } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Updates to tabular chunked display to force text content of cells. (fixes VCF display)
by Bitbucket 18 Apr '12

18 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/80014059ed11/ changeset: 80014059ed11 user: dannon date: 2012-04-19 00:32:23 summary: Updates to tabular chunked display to force text content of cells. (fixes VCF display) affected #: 1 file diff -r 7d6c2846c3c11157d05beb4f216d4efe5abd443f -r 80014059ed11eee51551b143d56780be2d234068 templates/dataset/tabular_chunked.mako --- a/templates/dataset/tabular_chunked.mako +++ b/templates/dataset/tabular_chunked.mako @@ -15,46 +15,46 @@ function renderCell(cell_contents, index, colspan){ if (colspan !== undefined){ - return '<td colspan="'+ colspan + '" class="stringalign">' + cell_contents + '</td>'; + return $('<td>').attr('colspan', colspan).addClass('stringalign').text(cell_contents); } else if (DATASET_TYPES[index] == 'str'){ /* Left align all str columns, right align the rest */ - return '<td class="stringalign">'+ cell_contents + '</td>'; + return $('<td>').addClass('stringalign').text(cell_contents);; } else{ - return '<td>'+ cell_contents + '</td>'; + return $('<td>').text(cell_contents); } } function renderRow(line){ /* Check length of cells to ensure this is a complete row. */ var cells = line.split('\t'); - var rowstr = '<tr>'; + var row = $('<tr>'); if (cells.length == DATASET_COLS){ $.each(cells, function(index, cell_contents){ - rowstr += renderCell(cell_contents, index); + row.append(renderCell(cell_contents, index)); }); } else if(cells.length > DATASET_COLS){ /* SAM file or like format with optional metadata included */ $.each(cells.slice(0, DATASET_COLS -1), function(index, cell_contents){ - rowstr += renderCell(cell_contents, index); + row.append(renderCell(cell_contents, index)); }); - rowstr += renderCell(cells.slice(DATASET_COLS -1).join('\t'), DATASET_COLS-1); + row.append(renderCell(cells.slice(DATASET_COLS -1).join('\t'), DATASET_COLS-1)); } else if(DATASET_COLS > 5 && cells.length == DATASET_COLS - 1 ){ /* SAM file or like format with optional metadata missing */ $.each(cells, function(index, cell_contents){ - rowstr += renderCell(cell_contents, index); + row.append(renderCell(cell_contents, index)); }); - rowstr += '<td></td>'; + row.append($('<td>')); } else{ + /* SAM file or like format with optional metadata missing */ /* Comment line, just return the one cell*/ - rowstr += renderCell(line, 0, DATASET_COLS); + row.append(renderCell(line, 0, DATASET_COLS)); } - rowstr += '</tr>'; - return rowstr; + return row; } function fillTable(){ 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: Enable interval datasets to be visualized in trackster.
by Bitbucket 18 Apr '12

18 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7d6c2846c3c1/ changeset: 7d6c2846c3c1 user: jgoecks date: 2012-04-18 22:59:14 summary: Enable interval datasets to be visualized in trackster. affected #: 3 files diff -r fbb7d4250604ddd0ed2c2006ab6601e6e973bd72 -r 7d6c2846c3c11157d05beb4f216d4efe5abd443f lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -328,6 +328,9 @@ def get_track_resolution( self, dataset, start, end): return None + + def get_track_type( self ): + return "FeatureTrack", {"data": "tabix", "index": "summary_tree"} class BedGraph( Interval ): """Tab delimited chrom/start/end/datavalue dataset""" diff -r fbb7d4250604ddd0ed2c2006ab6601e6e973bd72 -r 7d6c2846c3c11157d05beb4f216d4efe5abd443f lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -19,7 +19,7 @@ from galaxy.visualization.tracks.summary import * import galaxy_utils.sequence.vcf from galaxy.datatypes.tabular import Vcf -from galaxy.datatypes.interval import Bed, Gff, Gtf, ENCODEPeak +from galaxy.datatypes.interval import Interval, Bed, Gff, Gtf, ENCODEPeak from pysam import csamtools, ctabix @@ -67,8 +67,7 @@ """ Write data in region defined by chrom, start, and end to a file. """ - # Override. - pass + raise Exception( "Unimplemented Function" ) def valid_chroms( self ): """ @@ -81,23 +80,19 @@ Returns true if dataset has data in the specified genome window, false otherwise. """ - # Override. - pass + raise Exception( "Unimplemented Function" ) def get_iterator( self, chrom, start, end ): """ Returns an iterator that provides data in the region chrom:start-end """ - # Override. - pass + raise Exception( "Unimplemented Function" ) def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): """ Process data from an iterator to a format that can be provided to client. """ - # Override. - pass - + raise Exception( "Unimplemented Function" ) def get_data( self, chrom, start, end, start_val=0, max_vals=sys.maxint, **kwargs ): """ @@ -270,18 +265,96 @@ out.close() # +# -- Interval data providers -- +# + +class IntervalDataProvider( TracksDataProvider ): + """ + Processes BED data from native format to payload format. + + Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] + """ + + def get_iterator( self, chrom, start, end ): + raise Exception( "Unimplemented Function" ) + + def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): + """ + Provides + """ + # Build data to return. Payload format is: + # [ <guid/offset>, <start>, <end>, <name>, <strand> ] + # + # First three entries are mandatory, others are optional. + # + filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) + no_detail = ( "no_detail" in kwargs ) + rval = [] + message = None + # Subtract one b/c columns are 1-based but indices are 0-based. + col_fn = lambda col: None if col is None else col - 1 + start_col = self.original_dataset.metadata.startCol - 1 + end_col = self.original_dataset.metadata.endCol - 1 + strand_col = col_fn( self.original_dataset.metadata.strandCol ) + name_col = col_fn( self.original_dataset.metadata.nameCol ) + for count, line in enumerate( iterator ): + if count < start_val: + continue + if max_vals and count-start_val >= max_vals: + message = ERROR_MAX_VALS % ( max_vals, "features" ) + break + + feature = line.split() + length = len(feature) + # Unique id is just a hash of the line + payload = [ hash(line), int( feature[start_col] ), int( feature [end_col] ) ] + + if no_detail: + rval.append( payload ) + continue + + # Name, strand. + if name_col: + payload.append( feature[name_col] ) + if strand_col: + # Put empty name as placeholder. + if not name_col: payload.append( "" ) + payload.append( feature[strand_col] ) + + # Score (filter data) + if length >= 5 and filter_cols and filter_cols[0] == "Score": + try: + payload.append( float( feature[4] ) ) + except: + payload.append( feature[4] ) + + rval.append( payload ) + + return { 'data': rval, 'message': message } + + def write_data_to_file( self, chrom, start, end, filename ): + raise Exception( "Unimplemented Function" ) + +class IntervalTabixDataProvider( TabixDataProvider, IntervalDataProvider ): + """ + Provides data from a BED file indexed via tabix. + """ + pass + + +# # -- BED data providers -- # class BedDataProvider( TracksDataProvider ): """ - Abstract class that processes BED data from native format to payload format. + Processes BED data from native format to payload format. Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] """ def get_iterator( self, chrom, start, end ): - raise "Unimplemented Method" + raise Exception( "Unimplemented Method" ) def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): """ @@ -359,7 +432,7 @@ Provides data from a BED file indexed via tabix. """ pass - + class RawBedDataProvider( BedDataProvider ): """ Provide data from BED file. @@ -1113,7 +1186,12 @@ # type. First key is converted dataset type; if result is another dict, second key # is original dataset type. TODO: This needs to be more flexible. dataset_type_name_to_data_provider = { - "tabix": { Vcf: VcfTabixDataProvider, Bed: BedTabixDataProvider, ENCODEPeak: ENCODEPeakTabixDataProvider, "default" : TabixDataProvider }, + "tabix": { + Vcf: VcfTabixDataProvider, + Bed: BedTabixDataProvider, + ENCODEPeak: ENCODEPeakTabixDataProvider, + Interval: IntervalTabixDataProvider, + "default" : TabixDataProvider }, "interval_index": IntervalIndexDataProvider, "bai": BamDataProvider, "bam": SamDataProvider, diff -r fbb7d4250604ddd0ed2c2006ab6601e6e973bd72 -r 7d6c2846c3c11157d05beb4f216d4efe5abd443f static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -5655,7 +5655,7 @@ // -1 because end is not included in feature; see FeaturePainter documentation for details. feature_end = feature[2] - 1, feature_name = feature[3], - feature_strand = (feature.length > 4 ? feature[4] : null), + feature_strand = feature[4], f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), draw_start = f_start, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Fix missing sanitize_html import.
by Bitbucket 18 Apr '12

18 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fbb7d4250604/ changeset: fbb7d4250604 user: dannon date: 2012-04-18 22:30:11 summary: Fix missing sanitize_html import. affected #: 1 file diff -r fd33b522ceebbd0866f060b7309b14f9571ae06e -r fbb7d4250604ddd0ed2c2006ab6601e6e973bd72 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -3,6 +3,7 @@ from galaxy.util.odict import odict from galaxy.util.bunch import Bunch from galaxy.util import inflector +from galaxy.util.sanitize_html import sanitize_html from cgi import escape import metadata import zipfile 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 a running_functional_tests config setting.
by Bitbucket 18 Apr '12

18 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fd33b522ceeb/ changeset: fd33b522ceeb user: greg date: 2012-04-18 22:20:17 summary: Add a running_functional_tests config setting. affected #: 4 files diff -r aa821d6fdb3b56779401993727521acb661c90e8 -r fd33b522ceebbd0866f060b7309b14f9571ae06e lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -212,6 +212,7 @@ amqp_config = {} for k, v in amqp_config: self.amqp[k] = v + self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) ) def __read_tool_job_config( self, global_conf_parser, section, key ): try: tool_runners_config = global_conf_parser.items( section ) diff -r aa821d6fdb3b56779401993727521acb661c90e8 -r fd33b522ceebbd0866f060b7309b14f9571ae06e lib/galaxy/tool_shed/migrate/check.py --- a/lib/galaxy/tool_shed/migrate/check.py +++ b/lib/galaxy/tool_shed/migrate/check.py @@ -21,7 +21,6 @@ def verify_tools( app, url, galaxy_config_file, engine_options={} ): # Check the value in the migrate_tools.version database table column to verify that the number is in # sync with the number of version scripts in ~/lib/galaxy/tools/migrate/versions. - running_functional_tests = galaxy_config_file.endswith( '.sample' ) dialect = ( url.split( ':', 1 ) )[0] try: egg = dialect_to_egg[ dialect ] @@ -55,7 +54,7 @@ config_arg = '' if os.path.abspath( os.path.join( os.getcwd(), 'universe_wsgi.ini' ) ) != galaxy_config_file: config_arg = ' -c %s' % galaxy_config_file.replace( os.path.abspath( os.getcwd() ), '.' ) - if not running_functional_tests: + if not app.config.running_functional_tests: # Automatically update the value of the migrate_tools.version database table column. cmd = 'sh manage_tools.sh%s upgrade' % config_arg proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT ) diff -r aa821d6fdb3b56779401993727521acb661c90e8 -r fd33b522ceebbd0866f060b7309b14f9571ae06e lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -98,6 +98,7 @@ self.global_conf_parser = global_conf_parser if global_conf and "__file__" in global_conf: global_conf_parser.read(global_conf['__file__']) + self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) ) def get( self, key, default ): return self.config_dict.get( key, default ) def get_bool( self, key, default ): diff -r aa821d6fdb3b56779401993727521acb661c90e8 -r fd33b522ceebbd0866f060b7309b14f9571ae06e scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -275,6 +275,7 @@ library_import_dir = library_import_dir, user_library_import_dir = user_library_import_dir, global_conf = global_conf, + running_functional_tests=True, **kwargs ) log.info( "Embedded Universe application started" ) # ---- Run webserver ------------------------------------------------------ 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 spurious comments from templates.
by Bitbucket 18 Apr '12

18 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/aa821d6fdb3b/ changeset: aa821d6fdb3b user: jgoecks date: 2012-04-18 21:34:36 summary: Remove spurious comments from templates. affected #: 4 files diff -r 45bd2e0fe8d0eae68a82d3a141ebfc20d0ae7b2e -r aa821d6fdb3b56779401993727521acb661c90e8 templates/history/list_published.mako --- a/templates/history/list_published.mako +++ b/templates/history/list_published.mako @@ -24,8 +24,6 @@ <%def name="center_panel()"> - ## <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="page", action="list" )}"></iframe> - <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> ${h.to_unicode( grid )} diff -r 45bd2e0fe8d0eae68a82d3a141ebfc20d0ae7b2e -r aa821d6fdb3b56779401993727521acb661c90e8 templates/page/index.mako --- a/templates/page/index.mako +++ b/templates/page/index.mako @@ -11,8 +11,6 @@ <%def name="center_panel()"> - ## <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="page", action="list" )}"></iframe> - <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> ${h.to_unicode( grid )} diff -r 45bd2e0fe8d0eae68a82d3a141ebfc20d0ae7b2e -r aa821d6fdb3b56779401993727521acb661c90e8 templates/page/list_published.mako --- a/templates/page/list_published.mako +++ b/templates/page/list_published.mako @@ -24,8 +24,6 @@ <%def name="center_panel()"> - ## <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="page", action="list" )}"></iframe> - <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> ${h.to_unicode( grid )} diff -r 45bd2e0fe8d0eae68a82d3a141ebfc20d0ae7b2e -r aa821d6fdb3b56779401993727521acb661c90e8 templates/visualization/list_published.mako --- a/templates/visualization/list_published.mako +++ b/templates/visualization/list_published.mako @@ -24,8 +24,6 @@ <%def name="center_panel()"> - ## <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="page", action="list" )}"></iframe> - <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> ${h.to_unicode( grid )} 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: Fix decode issues with library datasets in Trackster.
by Bitbucket 18 Apr '12

18 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/45bd2e0fe8d0/ changeset: 45bd2e0fe8d0 user: jgoecks date: 2012-04-18 21:09:36 summary: Fix decode issues with library datasets in Trackster. affected #: 1 file diff -r 9e9f489c6488e63a5d8b86ae64a81c9b4ddd306d -r 45bd2e0fe8d0eae68a82d3a141ebfc20d0ae7b2e lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -322,7 +322,7 @@ if hda_ldda == "hda": dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) else: - dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id(dataset_id) ) + dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( dataset_id ) try: prefs = track_dict['prefs'] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for functinal tests when GALAXY_TEST_DBURI is not set in os.environ.
by Bitbucket 18 Apr '12

18 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9e9f489c6488/ changeset: 9e9f489c6488 user: greg date: 2012-04-18 20:29:01 summary: Fix for functinal tests when GALAXY_TEST_DBURI is not set in os.environ. affected #: 1 file diff -r 66c3172dff142cef1bdcecc257db797adc6e4584 -r 9e9f489c6488e63a5d8b86ae64a81c9b4ddd306d lib/galaxy/tool_shed/migrate/check.py --- a/lib/galaxy/tool_shed/migrate/check.py +++ b/lib/galaxy/tool_shed/migrate/check.py @@ -21,6 +21,7 @@ def verify_tools( app, url, galaxy_config_file, engine_options={} ): # Check the value in the migrate_tools.version database table column to verify that the number is in # sync with the number of version scripts in ~/lib/galaxy/tools/migrate/versions. + running_functional_tests = galaxy_config_file.endswith( '.sample' ) dialect = ( url.split( ':', 1 ) )[0] try: egg = dialect_to_egg[ dialect ] @@ -54,51 +55,52 @@ config_arg = '' if os.path.abspath( os.path.join( os.getcwd(), 'universe_wsgi.ini' ) ) != galaxy_config_file: config_arg = ' -c %s' % galaxy_config_file.replace( os.path.abspath( os.getcwd() ), '.' ) - # Automatically update the value of the migrate_tools.version database table column. - cmd = 'sh manage_tools.sh%s upgrade' % config_arg - proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT ) - return_code = proc.wait() - output = proc.stdout.read( 32768 ) - if return_code != 0: - raise Exception( "Error attempting to update the value of migrate_tools.version: %s" % output ) - elif missing_tool_configs: - if len( tool_panel_configs ) == 1: - plural = '' - tool_panel_config_file_names = tool_panel_configs[ 0 ] - else: - plural = 's' - tool_panel_config_file_names = ', '.join( tool_panel_configs ) - msg = "\n>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" - msg += "\n\nThe list of files at the end of this message refers to tools that are configured to load into the tool panel for\n" - msg += "this Galaxy instance, but have been removed from the Galaxy distribution. These tools can be automatically installed\n" - msg += "from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.\n\n" - msg += "To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this,\n" - msg += "be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should\n" - msg += "be removed from your file%s named %s.\n\n" % ( plural, tool_panel_config_file_names ) - msg += "CRITICAL NOTE IF YOU PLAN TO INSTALL\n" - msg += "The location in which the tool repositories will be installed is the value of the 'tool_path' attribute in the <tool>\n" - msg += 'tag of the file named ./migrated_tool_conf.xml (i.e., <toolbox tool_path="../shed_tools">). The default location\n' - msg += "setting is '../shed_tools', which may be problematic for some cluster environments, so make sure to change it before\n" - msg += "you execute the installation process if appropriate. The configured location must be outside of the Galaxy installation\n" - msg += "directory or it must be in a sub-directory protected by a properly configured .hgignore file if the directory is within\n" - msg += "the Galaxy installation directory hierarchy. This is because tool shed repositories will be installed using mercurial's\n" - msg += "clone feature, which creates .hg directories and associated mercurial repository files. Not having .hgignore properly\n" - msg += "configured could result in undesired behavior when modifying or updating your local Galaxy instance or the tool shed\n" - msg += "repositories if they are in directories that pose conflicts. See mercurial's .hgignore documentation at the following\n" - msg += "URL for details.\n\nhttp://mercurial.selenic.com/wiki/.hgignore\n\n" - msg += output - msg += "After the installation process finishes, you can start your Galaxy server. As part of this installation process,\n" - msg += "entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these\n" - msg += "tools will continue to be loaded into your tool panel. Because of this, existing entries for these files should be\n" - msg += "removed from your file%s named %s, but only after the installation process finishes.\n\n" % ( plural, tool_panel_config_file_names ) - for i, missing_tool_config in enumerate( missing_tool_configs ): - msg += "%s\n" % missing_tool_config - # Should we do the following? - #if i > 10: - # msg += "\n...and %d more tools...\n" % ( len( missing_tool_configs ) - ( i + 1 ) ) - # break - msg += "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n" - raise Exception( msg ) + if not running_functional_tests: + # Automatically update the value of the migrate_tools.version database table column. + cmd = 'sh manage_tools.sh%s upgrade' % config_arg + proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT ) + return_code = proc.wait() + output = proc.stdout.read( 32768 ) + if return_code != 0: + raise Exception( "Error attempting to update the value of migrate_tools.version: %s" % output ) + elif missing_tool_configs: + if len( tool_panel_configs ) == 1: + plural = '' + tool_panel_config_file_names = tool_panel_configs[ 0 ] + else: + plural = 's' + tool_panel_config_file_names = ', '.join( tool_panel_configs ) + msg = "\n>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" + msg += "\n\nThe list of files at the end of this message refers to tools that are configured to load into the tool panel for\n" + msg += "this Galaxy instance, but have been removed from the Galaxy distribution. These tools can be automatically installed\n" + msg += "from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.\n\n" + msg += "To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this,\n" + msg += "be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should\n" + msg += "be removed from your file%s named %s.\n\n" % ( plural, tool_panel_config_file_names ) + msg += "CRITICAL NOTE IF YOU PLAN TO INSTALL\n" + msg += "The location in which the tool repositories will be installed is the value of the 'tool_path' attribute in the <tool>\n" + msg += 'tag of the file named ./migrated_tool_conf.xml (i.e., <toolbox tool_path="../shed_tools">). The default location\n' + msg += "setting is '../shed_tools', which may be problematic for some cluster environments, so make sure to change it before\n" + msg += "you execute the installation process if appropriate. The configured location must be outside of the Galaxy installation\n" + msg += "directory or it must be in a sub-directory protected by a properly configured .hgignore file if the directory is within\n" + msg += "the Galaxy installation directory hierarchy. This is because tool shed repositories will be installed using mercurial's\n" + msg += "clone feature, which creates .hg directories and associated mercurial repository files. Not having .hgignore properly\n" + msg += "configured could result in undesired behavior when modifying or updating your local Galaxy instance or the tool shed\n" + msg += "repositories if they are in directories that pose conflicts. See mercurial's .hgignore documentation at the following\n" + msg += "URL for details.\n\nhttp://mercurial.selenic.com/wiki/.hgignore\n\n" + msg += output + msg += "After the installation process finishes, you can start your Galaxy server. As part of this installation process,\n" + msg += "entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these\n" + msg += "tools will continue to be loaded into your tool panel. Because of this, existing entries for these files should be\n" + msg += "removed from your file%s named %s, but only after the installation process finishes.\n\n" % ( plural, tool_panel_config_file_names ) + for i, missing_tool_config in enumerate( missing_tool_configs ): + msg += "%s\n" % missing_tool_config + # Should we do the following? + #if i > 10: + # msg += "\n...and %d more tools...\n" % ( len( missing_tool_configs ) - ( i + 1 ) ) + # break + msg += "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n" + raise Exception( msg ) else: log.info( "At migrate_tools version %d" % db_schema.version ) 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: Handle errors in the job handler caused by idata.hid being None.
by Bitbucket 18 Apr '12

18 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/66c3172dff14/ changeset: 66c3172dff14 user: natefoo date: 2012-04-18 20:15:52 summary: Handle errors in the job handler caused by idata.hid being None. affected #: 1 file diff -r d087c9f23f9bbf81176a253830b88cca15c458a7 -r 66c3172dff142cef1bdcecc257db797adc6e4584 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -207,14 +207,14 @@ continue # don't run jobs for which the input dataset was deleted if idata.deleted: - JobWrapper( job, self ).fail( "input data %d (file: %s) was deleted before the job started" % ( idata.hid, idata.file_name ) ) + JobWrapper( job, self ).fail( "input data %s (file: %s) was deleted before the job started" % ( idata.hid, idata.file_name ) ) return JOB_INPUT_DELETED # an error in the input data causes us to bail immediately elif idata.state == idata.states.ERROR: - JobWrapper( job, self ).fail( "input data %d is in error state" % ( idata.hid ) ) + JobWrapper( job, self ).fail( "input data %s is in error state" % ( idata.hid ) ) return JOB_INPUT_ERROR elif idata.state == idata.states.FAILED_METADATA: - JobWrapper( job, self ).fail( "input data %d failed to properly set metadata" % ( idata.hid ) ) + JobWrapper( job, self ).fail( "input data %s failed to properly set metadata" % ( idata.hid ) ) return JOB_INPUT_ERROR elif idata.state != idata.states.OK and not ( idata.state == idata.states.SETTING_METADATA and job.tool_id is not None and job.tool_id == self.app.datatypes_registry.set_external_metadata_tool.id ): # need to requeue Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for LibraryDatasetDatasetAssociation.templates_dict when a content value is not set.
by Bitbucket 18 Apr '12

18 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d087c9f23f9b/ changeset: d087c9f23f9b user: dan date: 2012-04-18 18:54:01 summary: Fix for LibraryDatasetDatasetAssociation.templates_dict when a content value is not set. affected #: 1 file diff -r 609b820ba1ea1ed753179b9228ca918b11969acf -r d087c9f23f9bbf81176a253830b88cca15c458a7 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1555,7 +1555,7 @@ name = field[ 'name' ] else: name = field[ 'label' ] - tmp_dict[ name ] = content[ field[ 'name' ] ] + tmp_dict[ name ] = content.get( field[ 'name' ] ) template_data[template.name] = tmp_dict return template_data def templates_json( self, use_name=False ): 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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