1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/2a8cb9436c2b/ changeset: r4984:2a8cb9436c2b user: dannon date: 2011-02-03 19:12:46 summary: Interval now uses line estimates instead of '? regions' for the peek. affected #: 2 files (116 bytes)
--- a/lib/galaxy/datatypes/data.py Thu Feb 03 09:34:39 2011 -0500 +++ b/lib/galaxy/datatypes/data.py Thu Feb 03 13:12:46 2011 -0500 @@ -397,6 +397,15 @@ if line and not line.startswith( '#' ): data_lines += 1 dataset.metadata.data_lines = data_lines + def estimate_file_lines( self, dataset ): + # Perform a rough estimate by extrapolating number of lines from a small read. + sample_size = 1048576 + dataset_fh = open( dataset.file_name ) + dataset_read = dataset_fh.read(sample_size) + dataset_fh.close() + sample_lines = dataset_read.count('\n') + est_lines = int(sample_lines * (float(dataset.get_size()) / float(sample_size))) + return est_lines def set_peek( self, dataset, line_count=None, is_multi_byte=False ): if not dataset.dataset.purged: # The file must exist on disk for the get_file_peek() method @@ -409,13 +418,7 @@ # Number of lines is not known ( this should not happen ), and auto-detect is # needed to set metadata # This can happen when the file is larger than max_optional_metadata_filesize. - # Perform a rough estimate by extrapolating number of lines from a small read. - sample_size = 1048576 - dataset_fh = open( dataset.file_name ) - dataset_read = dataset_fh.read(sample_size) - dataset_fh.close() - sample_lines = dataset_read.count('\n') - est_lines = int(sample_lines * (float(dataset.get_size()) / float(sample_size))) + est_lines = self.estimate_file_lines(dataset) dataset.blurb = "~%s %s" % ( util.commaify(str(est_lines)), inflector.cond_plural(est_lines, "line") ) else: dataset.blurb = "%s %s" % util.commaify( str(line_count) ), inflector.cond_plural(line_count, "line")
--- a/lib/galaxy/datatypes/interval.py Thu Feb 03 09:34:39 2011 -0500 +++ b/lib/galaxy/datatypes/interval.py Thu Feb 03 13:12:46 2011 -0500 @@ -71,7 +71,7 @@ else: # Number of lines is not known ( this should not happen ), and auto-detect is # needed to set metadata - dataset.blurb = "? regions" + dataset.blurb = "~%s regions" % util.commaify( str( self.estimate_file_lines(dataset) ) ) else: dataset.blurb = "%s regions" % util.commaify( str( line_count ) ) else:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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