Merge branch 'release_20.09' into dev

client/src/components/LibraryFolder/TopToolbar/FolderTopBar.vue

@@ -21,7 +21,6 @@
                     </button>
                     <div v-if="metadata.can_add_library_item">
                         <div
-                            v-if="multiple_add_dataset_options"
                             title="Add datasets to current folder"
                             class="dropdown add-library-items add-library-items-datasets mr-1"
                         >
@@ -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();
     },

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)

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()}]")
 

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

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):

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):

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)

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)

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):