diff --git a/client/src/components/LibraryFolder/TopToolbar/FolderTopBar.vue b/client/src/components/LibraryFolder/TopToolbar/FolderTopBar.vue index 9508c54f2be..202205ddbcf 100644 --- a/client/src/components/LibraryFolder/TopToolbar/FolderTopBar.vue +++ b/client/src/components/LibraryFolder/TopToolbar/FolderTopBar.vue @@ -21,7 +21,6 @@
@@ -201,7 +200,6 @@ export default { data() { return { is_admin: false, - multiple_add_dataset_options: false, user_library_import_dir: false, library_import_dir: false, allow_library_path_paste: false, @@ -227,13 +225,6 @@ export default { this.user_library_import_dir = Galaxy.config.user_library_import_dir; this.library_import_dir = Galaxy.config.library_import_dir; this.allow_library_path_paste = Galaxy.config.allow_library_path_paste; - if ( - this.user_library_import_dir !== null || - this.allow_library_path_paste !== false || - this.library_import_dir !== null - ) { - this.multiple_add_dataset_options = true; - } this.fetchExtAndGenomes(); }, diff --git a/client/src/components/Upload/UploadBoxMixin.js b/client/src/components/Upload/UploadBoxMixin.js index 09b2eb981e9..8904c84b29b 100644 --- a/client/src/components/Upload/UploadBoxMixin.js +++ b/client/src/components/Upload/UploadBoxMixin.js @@ -259,7 +259,7 @@ export default { return $(this.$refs.uploadTable); }, extensionDetails(extension) { - return findExtension(this.effectiveExtensions, extension); + return findExtension(this.app.effectiveExtensions, extension); }, initExtensionInfo() { $(this.$refs.footerExtensionInfo) diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py index 704506030ef..df1a9e6a074 100644 --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1940,10 +1940,13 @@ class JobWrapper(HasResourceParameters): return self.output_paths def get_output_path(self, dataset): + if getattr(dataset, "fake_dataset_association", False): + return dataset.file_name + assert dataset.id is not None, "{} needs to be flushed to find output path".format(dataset) if self.output_paths is None: self.compute_outputs() for (hda, dataset_path) in self.output_hdas_and_paths.values(): - if hda == dataset: + if hda.id == dataset.id: return dataset_path raise KeyError(f"Couldn't find job output for [{dataset}] in [{self.output_hdas_and_paths.values()}]") diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py index 7d0058ff189..183eca0629f 100644 --- a/lib/galaxy/managers/users.py +++ b/lib/galaxy/managers/users.py @@ -21,6 +21,7 @@ from galaxy.managers import ( deletable ) from galaxy.security.validate_user_input import ( + VALID_EMAIL_RE, validate_email, validate_password, validate_publicname @@ -278,6 +279,22 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin): raise exceptions.AuthenticationFailed(msg, **kwargs) return user + def get_user_by_identity(self, identity): + """Get user by username or email.""" + user = None + if VALID_EMAIL_RE.match(identity): + # VALID_PUBLICNAME and VALID_EMAIL do not overlap, so 'identity' here is an email address + user = self.session().query(self.model_class).filter( + self.model_class.table.c.email == identity).first() + if not user: + # Try a case-insensitive match on the email + user = self.session().query(self.model_class).filter( + func.lower(self.model_class.table.c.email) == identity.lower()).first() + else: + user = self.session().query(self.model_class).filter( + self.model_class.table.c.username == identity).first() + return user + # ---- current def current_user(self, trans): # define here for single point of change and make more readable diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py b/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py index 682c6755830..a5fd21bf284 100644 --- a/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py +++ b/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py @@ -15,9 +15,9 @@ from .mulled_build import ( add_build_arguments, add_single_image_arguments, args_to_mull_targets_kwds, - build_target, mull_targets, ) +from .util import build_target def main(argv=None): diff --git a/lib/galaxy/tool_util/deps/mulled/util.py b/lib/galaxy/tool_util/deps/mulled/util.py index 9535c400561..b3e68824dea 100644 --- a/lib/galaxy/tool_util/deps/mulled/util.py +++ b/lib/galaxy/tool_util/deps/mulled/util.py @@ -83,7 +83,7 @@ def mulled_tags_for(namespace, image, tag_prefix=None, resolution_cache=None): # Following check is pretty expensive against biocontainers... don't even bother doing it # if can't cache the response. if not _namespace_has_repo_name(namespace, image, resolution_cache): - log.debug("skipping mulled_tags_for [%s] no repository" % image) + log.info("skipping mulled_tags_for [%s] no repository" % image) return [] cache_key = "galaxy.tool_util.deps.container_resolvers.mulled.util:tag_cache" @@ -158,7 +158,8 @@ def build_target(package_name, version=None, build=None, tag=None): assert build is None version, build = split_tag(tag) - return Target(package_name, version, build, package_name) + # conda package and quay image names are lowercase + return Target(package_name.lower(), version, build, package_name) def conda_build_target_str(target): diff --git a/lib/galaxy/webapps/galaxy/api/authenticate.py b/lib/galaxy/webapps/galaxy/api/authenticate.py index 570ad83cc52..7b6d56a1757 100644 --- a/lib/galaxy/webapps/galaxy/api/authenticate.py +++ b/lib/galaxy/webapps/galaxy/api/authenticate.py @@ -15,7 +15,10 @@ from base64 import b64decode from urllib.parse import unquote from galaxy import exceptions -from galaxy.managers import api_keys +from galaxy.managers import ( + api_keys, + users, +) from galaxy.util import ( smart_str, unicodify @@ -30,6 +33,7 @@ class AuthenticationController(BaseAPIController): def __init__(self, app): super().__init__(app) + self.user_manager = users.UserManager(app) self.api_keys_manager = api_keys.ApiKeyManager(app) @expose_api_anonymous_and_sessionless @@ -58,18 +62,12 @@ class AuthenticationController(BaseAPIController): :raises: ObjectNotFound, HTTPBadRequest """ - email, password = self._decode_baseauth(trans.environ.get('HTTP_AUTHORIZATION')) - - user = trans.sa_session.query(trans.app.model.User).filter(trans.app.model.User.table.c.email == email).all() - - if len(user) == 0: + identity, password = self._decode_baseauth(trans.environ.get('HTTP_AUTHORIZATION')) + # check if this is an email address or username + user = self.user_manager.get_user_by_identity(identity) + if not user: raise exceptions.ObjectNotFound('The user does not exist.') - elif len(user) > 1: - # DB is inconsistent and we have more users with the same email. - raise exceptions.InconsistentDatabase('An error occurred, please contact your administrator.') - else: - user = user[0] - is_valid_user = self.app.auth_manager.check_password(user, password) + is_valid_user = self.app.auth_manager.check_password(user, password) if is_valid_user: key = self.api_keys_manager.get_or_create_api_key(user) return dict(api_key=key) diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py index 84de563132b..2e7114c5f2c 100644 --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -7,10 +7,6 @@ from datetime import datetime, timedelta from urllib.parse import unquote from markupsafe import escape -from sqlalchemy import ( - func, - or_ -) from sqlalchemy.orm.exc import NoResultFound from galaxy import ( @@ -134,15 +130,7 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesApiKeysMixin): status = None if not login or not password: return self.message_exception(trans, "Please specify a username and password.") - user = trans.sa_session.query(trans.app.model.User).filter(or_( - trans.app.model.User.table.c.email == login, - trans.app.model.User.table.c.username == login - )).first() - if not user: - # Try a case-insensitive match on the email - user = trans.sa_session.query(trans.app.model.User).filter( - func.lower(trans.app.model.User.table.c.email) == login.lower() - ).first() + user = self.user_manager.get_user_by_identity(login) log.debug("trans.app.config.auth_config_file: %s" % trans.app.config.auth_config_file) if user is None: message, user = self.__autoregistration(trans, login, password) diff --git a/test/unit/managers/test_UserManager.py b/test/unit/managers/test_UserManager.py index a65315040c8..f79274ca0c9 100644 --- a/test/unit/managers/test_UserManager.py +++ b/test/unit/managers/test_UserManager.py @@ -23,6 +23,8 @@ changed_password = '654321' user2_data = dict(email='user2@user2.user2', username='user2', password=default_password) user3_data = dict(email='user3@user3.user3', username='user3', password=default_password) user4_data = dict(email='user4@user4.user4', username='user4', password=default_password) +uppercase_email_user = dict(email='USER5@USER5.USER5', username='USER5', password=default_password) +lowercase_email_user = dict(email='user5@user5.user5', username='user5', password=default_password) # ============================================================================= @@ -192,6 +194,31 @@ class UserManagerTestCase(BaseTestCase): self.assertFalse(check_password("", user.password)) self.assertFalse(check_password(None, user.password)) + def test_get_user_by_identity(self): + # return None if username/email not found + assert self.user_manager.get_user_by_identity('xyz') is None + uppercase_user = self.user_manager.create(**uppercase_email_user) + assert uppercase_user.email == uppercase_email_user['email'] + assert uppercase_user.username == uppercase_email_user['username'] + assert self.user_manager.get_user_by_identity(uppercase_user.email) == uppercase_user + assert self.user_manager.get_user_by_identity(uppercase_user.username) == uppercase_user + # Create another user with the same email just differently capitalized. + # This is not normally allowed now, since registration goes through user_manager.register(), + # which checks for that, but was possible in earlier releases of Galaxy + lowercase_user = self.user_manager.create(**lowercase_email_user) + assert lowercase_user.email == lowercase_email_user['email'] + assert lowercase_user.username == lowercase_email_user['username'] + assert self.user_manager.get_user_by_identity(lowercase_user.email) == lowercase_user + assert self.user_manager.get_user_by_identity(lowercase_user.username) == lowercase_user + # assert uppercase user can still be retrieved + assert self.user_manager.get_user_by_identity(uppercase_user.email) == uppercase_user + assert self.user_manager.get_user_by_identity(uppercase_user.username) == uppercase_user + # username matches need to be exact + assert self.user_manager.get_user_by_identity(uppercase_user.username.capitalize()) is None + # email matches can ignore capitalization + ignore_email_capitalization_user = self.user_manager.create(email='user123@nopassword.com', username='someusername123') + assert self.user_manager.get_user_by_identity(ignore_email_capitalization_user.email.capitalize()) == ignore_email_capitalization_user + # ============================================================================= class UserSerializerTestCase(BaseTestCase):