1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ba59dcfc3db0/ Changeset: ba59dcfc3db0 Branch: next-stable User: jjohnson Date: 2014-10-02 18:34:49+00:00 Summary: SQlite needs to import re and sqlite in order to set metadata Affected #: 1 file diff -r 99bc7d90156facd280def33e6ad7e303ebe8d838 -r ba59dcfc3db0a95f2e2b906eac1971e31c2db4ee lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -11,12 +11,14 @@ import struct import subprocess import tempfile +import re from galaxy import eggs eggs.require( "bx-python" ) from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP, TWOBIT_MAGIC_SIZE +from galaxy.util import sqlite from galaxy.datatypes.metadata import MetadataElement,ListParameter,DictParameter from galaxy.datatypes import metadata import dataproviders @@ -560,7 +562,7 @@ tables = [] columns = dict() rowcounts = dict() - conn = sqlite3.connect(dataset.file_name) + conn = sqlite.connect(dataset.file_name) c = conn.cursor() tables_query = "SELECT name,sql FROM sqlite_master WHERE type='table' ORDER BY name" rslt = c.execute(tables_query).fetchall() @@ -574,7 +576,7 @@ dataset.metadata.table_columns = columns dataset.metadata.table_row_count = rowcounts except Exception, exc: - pass + log.warn( '%s, set_meta Exception: %s', self, exc ) def sniff( self, filename ): # The first 16 bytes of any SQLite3 database file is 'SQLite format 3\0', and the file is binary. For details 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.