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)); }

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