2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/0bb5714cb801/
Changeset: 0bb5714cb801
User: lepsiobec
Date: 2013-12-18 19:59:20
Summary: aiding security flaw with downloading datasets in archives
Affected #: 1 file
diff -r cbd1387437ceba5be9b47dcbf9eb951086e410a1 -r 0bb5714cb8012515824fd3e435b683afd554cdd2 lib/galaxy/webapps/galaxy/controllers/library_common.py
--- a/lib/galaxy/webapps/galaxy/controllers/library_common.py
+++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py
@@ -18,7 +18,7 @@
from galaxy.util import inflector
from galaxy.util.json import to_json_string, from_json_string
from galaxy.util.streamball import StreamBall
-from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin
+from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin, UsesLibraryMixinItems
from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, build_select_field
from galaxy.model.orm import and_, eagerload_all
@@ -65,7 +65,7 @@
except:
pass
-class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin ):
+class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin, UsesLibraryMixinItems ):
@web.json
def library_item_updates( self, trans, ids=None, states=None ):
# Avoid caching
@@ -1750,7 +1750,8 @@
ldda_ids = util.listify( ldda_ids )
for ldda_id in ldda_ids:
try:
- ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) )
+ # Load the ldda requested and check whether the user has access to them
+ ldda = self.get_library_dataset_dataset_association( trans, ldda_id )
assert not ldda.dataset.purged
lddas.append( ldda )
except:
https://bitbucket.org/galaxy/galaxy-central/commits/0b2676366a82/
Changeset: 0b2676366a82
User: lepsiobec
Date: 2013-12-18 20:08:19
Summary: Merge
Affected #: 1 file
diff -r 0bb5714cb8012515824fd3e435b683afd554cdd2 -r 0b2676366a82d61b5e46f4cae6a235e643548f78 install_and_test_tool_shed_repositories.sh
--- a/install_and_test_tool_shed_repositories.sh
+++ b/install_and_test_tool_shed_repositories.sh
@@ -13,6 +13,10 @@
# If the tool shed url is not specified in tool_sheds_conf.xml, GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF must be set to
# a tool sheds configuration file that does specify that url or repository installation will fail.
+# This script accepts the command line option -w to select which set of tests to run. The default behavior is to test
+# first tool_dependency_definition repositories and then repositories with tools. Provide the value 'dependencies'
+# to test only tool_dependency_definition repositories or 'tools' to test only repositories with tools.
+
if [ -z $GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY ] ; then
echo "This script requires the GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY environment variable to be set and non-empty."
exit 1
@@ -39,14 +43,41 @@
fi
fi
-# Test installation of repositories of type tool_dependency_definition.
-python test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py $* -v --with-nosehtml --html-report-file \
- test/install_and_test_tool_shed_repositories/tool_dependency_definitions/run_functional_tests.html \
- test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \
- test/functional/test_toolbox.py
+test_tool_dependency_definitions () {
+ # Test installation of repositories of type tool_dependency_definition.
+ python test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py $* -v --with-nosehtml --html-report-file \
+ test/install_and_test_tool_shed_repositories/tool_dependency_definitions/run_functional_tests.html \
+ test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \
+ test/functional/test_toolbox.py
+}
-# Test installation of repositories that contain valid tools with defined functional tests and a test-data directory containing test files.
-#python test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py $* -v --with-nosehtml --html-report-file \
-# test/install_and_test_tool_shed_repositories/repositories_with_tools/run_functional_tests.html \
-# test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \
-# test/functional/test_toolbox.py
+test_repositories_with_tools () {
+ # Test installation of repositories that contain valid tools with defined functional tests and a test-data directory containing test files.
+ python test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py $* -v --with-nosehtml --html-report-file \
+ test/install_and_test_tool_shed_repositories/repositories_with_tools/run_functional_tests.html \
+ test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \
+ test/functional/test_toolbox.py
+}
+
+which='both'
+
+while getopts "w:" arg; do
+ case $arg in
+ w)
+ which=$OPTARG
+ ;;
+ esac
+done
+
+case $which in
+ dependencies)
+ test_tool_dependency_definitions
+ ;;
+ tools)
+ test_repositories_with_tools
+ ;;
+ *)
+ test_tool_dependency_definitions
+ test_repositories_with_tools
+ ;;
+esac
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/9c17939bb282/
Changeset: 9c17939bb282
User: inithello
Date: 2013-12-18 19:53:18
Summary: Add command line option to select which set of tests to run.
Affected #: 1 file
diff -r cbd1387437ceba5be9b47dcbf9eb951086e410a1 -r 9c17939bb28242a1532daf2c24c2920786b3502f install_and_test_tool_shed_repositories.sh
--- a/install_and_test_tool_shed_repositories.sh
+++ b/install_and_test_tool_shed_repositories.sh
@@ -13,6 +13,10 @@
# If the tool shed url is not specified in tool_sheds_conf.xml, GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF must be set to
# a tool sheds configuration file that does specify that url or repository installation will fail.
+# This script accepts the command line option -w to select which set of tests to run. The default behavior is to test
+# first tool_dependency_definition repositories and then repositories with tools. Provide the value 'dependencies'
+# to test only tool_dependency_definition repositories or 'tools' to test only repositories with tools.
+
if [ -z $GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY ] ; then
echo "This script requires the GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY environment variable to be set and non-empty."
exit 1
@@ -39,14 +43,41 @@
fi
fi
-# Test installation of repositories of type tool_dependency_definition.
-python test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py $* -v --with-nosehtml --html-report-file \
- test/install_and_test_tool_shed_repositories/tool_dependency_definitions/run_functional_tests.html \
- test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \
- test/functional/test_toolbox.py
+test_tool_dependency_definitions () {
+ # Test installation of repositories of type tool_dependency_definition.
+ python test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py $* -v --with-nosehtml --html-report-file \
+ test/install_and_test_tool_shed_repositories/tool_dependency_definitions/run_functional_tests.html \
+ test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \
+ test/functional/test_toolbox.py
+}
-# Test installation of repositories that contain valid tools with defined functional tests and a test-data directory containing test files.
-#python test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py $* -v --with-nosehtml --html-report-file \
-# test/install_and_test_tool_shed_repositories/repositories_with_tools/run_functional_tests.html \
-# test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \
-# test/functional/test_toolbox.py
+test_repositories_with_tools () {
+ # Test installation of repositories that contain valid tools with defined functional tests and a test-data directory containing test files.
+ python test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py $* -v --with-nosehtml --html-report-file \
+ test/install_and_test_tool_shed_repositories/repositories_with_tools/run_functional_tests.html \
+ test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \
+ test/functional/test_toolbox.py
+}
+
+which='both'
+
+while getopts "w:" arg; do
+ case $arg in
+ w)
+ which=$OPTARG
+ ;;
+ esac
+done
+
+case $which in
+ dependencies)
+ test_tool_dependency_definitions
+ ;;
+ tools)
+ test_repositories_with_tools
+ ;;
+ *)
+ test_tool_dependency_definitions
+ test_repositories_with_tools
+ ;;
+esac
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/cbd1387437ce/
Changeset: cbd1387437ce
User: inithello
Date: 2013-12-18 19:14:24
Summary: Another bugfix to the tool dependency cleaning script.
Affected #: 1 file
diff -r d1b1558308dc1cbb8076d20a7b7d130ca4051e1d -r cbd1387437ceba5be9b47dcbf9eb951086e410a1 lib/tool_shed/scripts/clean_up_tool_dependency_directory.py
--- a/lib/tool_shed/scripts/clean_up_tool_dependency_directory.py
+++ b/lib/tool_shed/scripts/clean_up_tool_dependency_directory.py
@@ -11,10 +11,11 @@
else:
for content in os.listdir( args.tool_dependency_dir ):
print 'Deleting directory %s from %s.' % ( content, args.tool_dependency_dir )
- if os.path.isdir( content ):
- shutil.rmtree( os.path.join( args.tool_dependency_dir, content ) )
+ full_path = os.path.join( args.tool_dependency_dir, content )
+ if os.path.isdir( full_path ):
+ shutil.rmtree( full_path )
else:
- os.remove( content )
+ os.remove( full_path )
if __name__ == '__main__':
description = 'Clean out the configured tool dependency path, creating it if it does not exist.'
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d1b1558308dc/
Changeset: d1b1558308dc
User: inithello
Date: 2013-12-18 19:11:37
Summary: Fix error when attempting to remove a file.
Affected #: 1 file
diff -r c4c6e8ea9837d4aa4fbbf08a681fd0c72b34f5b6 -r d1b1558308dc1cbb8076d20a7b7d130ca4051e1d lib/tool_shed/scripts/clean_up_tool_dependency_directory.py
--- a/lib/tool_shed/scripts/clean_up_tool_dependency_directory.py
+++ b/lib/tool_shed/scripts/clean_up_tool_dependency_directory.py
@@ -9,9 +9,12 @@
os.mkdir( args.tool_dependency_dir )
return 0
else:
- for subdirectory in os.listdir( args.tool_dependency_dir ):
- print 'Deleting directory %s from %s.' % ( subdirectory, args.tool_dependency_dir )
- shutil.rmtree( os.path.join( args.tool_dependency_dir, subdirectory ) )
+ for content in os.listdir( args.tool_dependency_dir ):
+ print 'Deleting directory %s from %s.' % ( content, args.tool_dependency_dir )
+ if os.path.isdir( content ):
+ shutil.rmtree( os.path.join( args.tool_dependency_dir, content ) )
+ else:
+ os.remove( content )
if __name__ == '__main__':
description = 'Clean out the configured tool dependency path, creating it if it does not exist.'
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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