From 50e531aa5971bee6f727ad0013b45c4a5d052fc9 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 17 Dec 2015 15:32:45 +0000 Subject: [PATCH] Refactor galaxy.datatypes.checkers into galaxy.util.checkers. - Primary reason is because it is used all over the place in contexts that have nothing to do with Galaxy datatype classes or datatype registery or sniffing, most importantly by the code in the tool shed for determining if something is a tool or not. - This code has no dependencies on the datatypes module or any hard dependencies on things not in the Python standard library. --- lib/galaxy/datatypes/converters/fastq_to_fqtoc.py | 2 +- lib/galaxy/datatypes/sequence.py | 2 +- lib/galaxy/datatypes/sniff.py | 2 +- lib/galaxy/datatypes/tabular.py | 2 +- lib/galaxy/{datatypes => util}/checkers.py | 0 lib/galaxy/webapps/tool_shed/api/repositories.py | 2 +- lib/galaxy/webapps/tool_shed/controllers/upload.py | 2 +- lib/tool_shed/metadata/metadata_generator.py | 2 +- lib/tool_shed/util/commit_util.py | 2 +- lib/tool_shed/util/shed_util_common.py | 2 +- lib/tool_shed/util/tool_util.py | 2 +- tools/data_source/upload.py | 2 +- 12 files changed, 11 insertions(+), 11 deletions(-) rename lib/galaxy/{datatypes => util}/checkers.py (100%) diff --git a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py index ba6ba4079d1..bb9f0b488a9 100644 --- a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py +++ b/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(): diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py index 720c10c513b..f6197a96628 100644 --- a/lib/galaxy/datatypes/sequence.py +++ b/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 diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py index 560e8100fc2..5683c804e37 100644 --- a/lib/galaxy/datatypes/sniff.py +++ b/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__) diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py index 2c4bf3be072..3617ed5336a 100644 --- a/lib/galaxy/datatypes/tabular.py +++ b/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 diff --git a/lib/galaxy/datatypes/checkers.py b/lib/galaxy/util/checkers.py similarity index 100% rename from lib/galaxy/datatypes/checkers.py rename to lib/galaxy/util/checkers.py diff --git a/lib/galaxy/webapps/tool_shed/api/repositories.py b/lib/galaxy/webapps/tool_shed/api/repositories.py index d27a917fa23..08a8c697bf2 100644 --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/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 diff --git a/lib/galaxy/webapps/tool_shed/controllers/upload.py b/lib/galaxy/webapps/tool_shed/controllers/upload.py index d6876ef8345..f824c5f0dff 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/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 diff --git a/lib/tool_shed/metadata/metadata_generator.py b/lib/tool_shed/metadata/metadata_generator.py index 5f7e3cb38a1..561036ea08f 100644 --- a/lib/tool_shed/metadata/metadata_generator.py +++ b/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 diff --git a/lib/tool_shed/util/commit_util.py b/lib/tool_shed/util/commit_util.py index 4738cdd9314..e0ad20a2805 100644 --- a/lib/tool_shed/util/commit_util.py +++ b/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 diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py index 4fb2f18c573..82256715c98 100644 --- a/lib/tool_shed/util/shed_util_common.py +++ b/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 diff --git a/lib/tool_shed/util/tool_util.py b/lib/tool_shed/util/tool_util.py index 10fec0e2f5c..9df2d6a347e 100644 --- a/lib/tool_shed/util/tool_util.py +++ b/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 diff --git a/tools/data_source/upload.py b/tools/data_source/upload.py index 086e81a9afd..625a3cd974e 100644 --- a/tools/data_source/upload.py +++ b/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