moved common_util.py, encoding_util.py and xml_util.py from tool_shed/util to galaxy/util/tool_shed (for data package)

lib/galaxy/datatypes/converters/maf_to_fasta_converter.py

@@ -6,7 +6,7 @@ import sys
 
 import bx.align.maf
 
-from galaxy.tools.util import maf_utilities
+from galaxy.datatypes.util import maf_utilities
 
 assert sys.version_info[:2] >= (2, 6)
 

lib/galaxy/datatypes/converters/maf_to_interval_converter.py

@@ -6,7 +6,7 @@ import sys
 
 import bx.align.maf
 
-from galaxy.tools.util import maf_utilities
+from galaxy.datatypes.util import maf_utilities
 
 assert sys.version_info[:2] >= (2, 6)
 

lib/galaxy/datatypes/test/temp2.txt

@@ -0,0 +1,2 @@
+1 2
+3 4

lib/galaxy/model/migrate/check.py

@@ -1,6 +1,5 @@
 import logging
 import os.path
-import sys
 
 from migrate.versioning import repository, schema
 from sqlalchemy import (

lib/galaxy/model/tool_shed_install/__init__.py

@@ -4,7 +4,7 @@ import os
 from galaxy.util import asbool
 from galaxy.util.bunch import Bunch
 from galaxy.util.dictifiable import Dictifiable
-from tool_shed.util import common_util
+from galaxy.util.tool_shed import common_util
 
 log = logging.getLogger(__name__)
 

lib/galaxy/util/tool_shed/common_util.py

@@ -1,13 +1,15 @@
 import json
 import logging
 import os
+import sys
+
+from routes import url_for
 
 from six.moves.urllib.parse import urljoin
 
 from galaxy import util
 from galaxy.util.odict import odict
-from galaxy.web import url_for
-from tool_shed.util import encoding_util, xml_util
+from galaxy.util.tool_shed import encoding_util, xml_util
 
 log = logging.getLogger(__name__)
 

lib/galaxy/util/tool_shed/encoding_util.py

@@ -1,6 +1,5 @@
 import binascii
 import json
-import logging
 
 from galaxy.util import (
     smart_str,
@@ -8,7 +7,6 @@ from galaxy.util import (
 )
 from galaxy.util.hash_util import hmac_new
 
-log = logging.getLogger(__name__)
 
 encoding_sep = '__esep__'
 encoding_sep2 = '__esepii__'

packages/data/requirements.txt

@@ -1,13 +1,16 @@
 galaxy-objectstore
+galaxy-sequence-utils==1.1.3
 galaxy-util
 bdbag
 bx-python
 h5py
 isa-rwval
 numpy
+parsley
 pycryptodome
 pysam
 social_auth_core
 SQLAlchemy==1.2
 sqlalchemy-migrate
+sqlalchemy-utils
 WebOb

packages/data/tests/unittest_utils/__init__.py

@@ -1 +1 @@
-../../test/unit/unittest_utils/__init__.py
+../../../../test/unit/unittest_utils/__init__.py

packages/data/tests/unittest_utils/tempfilecache.py

@@ -1 +1 @@
-../../test/unit/unittest_utils/tempfilecache.py
+../../../../test/unit/unittest_utils/tempfilecache.py

packages/data/tests/unittest_utils/utility.py

@@ -1 +1 @@
-../../test/unit/unittest_utils/utility.py
+../../../../test/unit/unittest_utils/utility.py

packages/util/requirements.txt

@@ -2,7 +2,9 @@ bleach
 boltons
 bz2file; python_version < '3.3'
 docutils
+logging
 markupsafe
 packaging
 pyyaml
+routes
 six>=1.9.0