3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5623c1027c64/ Changeset: 5623c1027c64 User: dannon Date: 2013-08-30 04:35:20 Summary: Cleanup imports in sniff.py Affected #: 1 file diff -r ce2528c40e4d89642bc98c2aff7bdc6f524e4f03 -r 5623c1027c6490b84fb35a6dd3897337153f8ec5 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -1,12 +1,21 @@ """ File format detector """ -import logging, sys, os, csv, tempfile, shutil, re, zipfile, gzip +import gzip +import logging +import os +import re import registry +import shutil +import sys +import tempfile +import zipfile + +from encodings import search_function as encodings_search_function + from galaxy import util -from galaxy.datatypes.checkers import * -from encodings import search_function as encodings_search_function -from binary import Binary +from galaxy.datatypes.checkers import check_binary, check_html, is_gzip +from galaxy.datatypes.binary import Binary log = logging.getLogger(__name__) @@ -405,5 +414,5 @@ pass if __name__ == '__main__': - import doctest, sys + import doctest doctest.testmod(sys.modules[__name__]) https://bitbucket.org/galaxy/galaxy-central/commits/53f78e82f398/ Changeset: 53f78e82f398 User: dannon Date: 2013-08-30 04:36:33 Summary: Flag duplicated code in workflows API (basically copied straight from controllers/workflow.py) -- needs refactor. Affected #: 1 file diff -r 5623c1027c6490b84fb35a6dd3897337153f8ec5 -r 53f78e82f398067349d2c37c1e0281846be72a31 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -453,6 +453,11 @@ ### ----------------------------------- ### ## RPARK EDIT ## + + # TODO: This is duplicated from + # lib/galaxy/webapps/controllres/workflow.py -- refactor and + # eliminate copied code. + # Get user annotation. step_annotation = self.get_item_annotation_obj(trans.sa_session, trans.user, step ) annotation_str = "" https://bitbucket.org/galaxy/galaxy-central/commits/a1abf7b75d3e/ Changeset: a1abf7b75d3e User: dannon Date: 2013-08-30 04:38:22 Summary: Clarify in maf_utilities that there now no longer exists a duplicate method in datatypes/sequence.py. Affected #: 1 file diff -r 53f78e82f398067349d2c37c1e0281846be72a31 -r a1abf7b75d3e28ee0dc800a2ba13498e45d70ca2 lib/galaxy/tools/util/maf_utilities.py --- a/lib/galaxy/tools/util/maf_utilities.py +++ b/lib/galaxy/tools/util/maf_utilities.py @@ -187,7 +187,6 @@ except: return build_maf_index( maf_file, species = species ) -#*** ANYCHANGE TO THIS METHOD HERE OR IN galaxy.datatypes.sequences MUST BE PROPAGATED *** def build_maf_index_species_chromosomes( filename, index_species = None ): species = [] species_chromosomes = {} 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.