Merge pull request #1363 from jmchilton/checkers_refactor

Refactor galaxy.datatypes.checkers into galaxy.util.checkers.

lib/galaxy/datatypes/converters/fastq_to_fqtoc.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 import sys
-from galaxy.datatypes.checkers import is_gzip
+from galaxy.util.checkers import is_gzip
 
 
 def main():

lib/galaxy/datatypes/sequence.py

@@ -12,7 +12,7 @@ from cgi import escape
 
 from galaxy import util
 from galaxy.datatypes import metadata
-from galaxy.datatypes.checkers import is_gzip
+from galaxy.util.checkers import is_gzip
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.sniff import get_headers
 from galaxy.datatypes.util.image_util import check_image_type

lib/galaxy/datatypes/sniff.py

@@ -15,7 +15,7 @@ from encodings import search_function as encodings_search_function
 
 from galaxy import util
 from galaxy.util import multi_byte
-from galaxy.datatypes.checkers import check_binary, check_html, is_gzip
+from galaxy.util.checkers import check_binary, check_html, is_gzip
 from galaxy.datatypes.binary import Binary
 
 log = logging.getLogger(__name__)

lib/galaxy/datatypes/tabular.py

@@ -13,7 +13,7 @@ from cgi import escape
 
 from galaxy import util
 from galaxy.datatypes import data, metadata
-from galaxy.datatypes.checkers import is_gzip
+from galaxy.util.checkers import is_gzip
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.sniff import get_headers
 from galaxy.util.json import dumps

lib/galaxy/webapps/tool_shed/api/repositories.py

@@ -11,7 +11,7 @@ from sqlalchemy import and_, false
 
 from galaxy import util
 from galaxy import web
-from galaxy.datatypes import checkers
+from galaxy.util import checkers
 from galaxy.exceptions import ActionInputError
 from galaxy.exceptions import ConfigDoesNotAllowException
 from galaxy.exceptions import InsufficientPermissionsException

lib/galaxy/webapps/tool_shed/controllers/upload.py

@@ -7,7 +7,7 @@ import urllib
 
 from galaxy import util
 from galaxy import web
-from galaxy.datatypes import checkers
+from galaxy.util import checkers
 from galaxy.web.base.controller import BaseUIController
 from tool_shed.util.web_util import escape
 

lib/tool_shed/metadata/metadata_generator.py

@@ -6,7 +6,7 @@ import tempfile
 from sqlalchemy import and_
 
 from galaxy import util
-from galaxy.datatypes import checkers
+from galaxy.util import checkers
 from galaxy.tools.data_manager.manager import DataManager
 from galaxy.tools.parser.interface import TestCollectionDef
 from galaxy.web import url_for

lib/tool_shed/util/commit_util.py

@@ -9,7 +9,7 @@ import tempfile
 from sqlalchemy.sql.expression import null
 
 import tool_shed.repository_types.util as rt_util
-from galaxy.datatypes import checkers
+from galaxy.util import checkers
 from tool_shed.tools import data_table_manager
 from tool_shed.util import basic_util, hg_util, shed_util_common as suc
 

lib/tool_shed/util/shed_util_common.py

@@ -12,7 +12,7 @@ from sqlalchemy import and_, false, or_, true
 
 from galaxy import util
 from galaxy.web import url_for
-from galaxy.datatypes import checkers
+from galaxy.util import checkers
 from tool_shed.util import basic_util
 from tool_shed.util import common_util
 from tool_shed.util import encoding_util

lib/tool_shed/util/tool_util.py

@@ -4,7 +4,7 @@ import shutil
 
 import galaxy.tools
 from galaxy import util
-from galaxy.datatypes import checkers
+from galaxy.util import checkers
 from galaxy.util.expressions import ExpressionContext
 from galaxy.web.form_builder import SelectField
 

tools/data_source/upload.py

@@ -18,11 +18,11 @@ from galaxy import util
 import galaxy.model  # noqa
 from galaxy.datatypes import sniff
 from galaxy.datatypes.binary import Binary
-from galaxy.datatypes.checkers import check_binary, check_bz2, check_gzip, check_html, check_image, check_zip
 from galaxy.datatypes.registry import Registry
 from galaxy.datatypes.util.image_util import get_image_ext
 from galaxy.util.json import dumps, loads
 from galaxy.util import multi_byte
+from galaxy.util.checkers import check_binary, check_bz2, check_gzip, check_html, check_image, check_zip
 
 try:
     import Image as PIL