1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/bea6f76a652e/ changeset: bea6f76a652e user: dannon date: 2012-12-04 20:14:28 summary: Tabular Display: For extremely wide datasets, revert to the old behavior until we have a proper 'matrix' datatype w/ renderer. Cleanup/imports. affected #: 1 file
diff -r 3a1f833d3463ff3b5fc82eeff5adc72f1a07c6a9 -r bea6f76a652e8f47e97c0995986bda8e939f714e lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -4,15 +4,16 @@ """ import pkg_resources pkg_resources.require( "bx-python" ) - +import gzip import logging -import data +import os +from cgi import escape from galaxy import util -from cgi import escape +from galaxy.datatypes import data from galaxy.datatypes import metadata +from galaxy.datatypes.checkers import is_gzip from galaxy.datatypes.metadata import MetadataElement -import galaxy_utils.sequence.vcf -from sniff import * +from galaxy.datatypes.sniff import get_headers from galaxy.util.json import to_json_string
log = logging.getLogger(__name__) @@ -264,10 +265,21 @@ return to_json_string({'ck_data': ck_data, 'ck_index': ck_index+1})
def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None): - #TODO Prevent failure when displaying extremely long > 50kb lines. if chunk: return self.get_chunk(trans, dataset, chunk) - if to_ext or not preview: + elif dataset.metadata.columns > 50: + #Fancy tabular display is only suitable for datasets without an incredibly large number of columns. + #We should add a new datatype 'matrix', with it's own draw method, suitable for this kind of data. + #For now, default to the old behavior, ugly as it is. Remove this after adding 'matrix'. + max_peek_size = 1000000 # 1 MB + if not preview or os.stat( dataset.file_name ).st_size < max_peek_size: + return open( dataset.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) + elif to_ext or not preview: return self._serve_raw(trans, dataset, to_ext) else: column_names = 'null' @@ -589,7 +601,6 @@ - LANE, TILEm X, Y, INDEX, READ_NO, SEQ, QUAL, POSITION, *STRAND, FILT must be correct - We will only check that up to the first 5 alignments are correctly formatted. """ - import gzip try: compress = is_gzip(filename) if compress:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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