Do not initialize a full repository registry in ToolShed 2.0.

It seems like it is only used by repository_grids - which I think are unused by the new tool shed. I don't recall writing any client side grid framework code and my PR description did claim it was mako free.

lib/tool_shed/managers/categories.py

@@ -59,9 +59,7 @@ class CategoryManager:
 
     def to_dict(self, category: Category) -> Dict[str, Any]:
         category_dict = category.to_dict(view="collection", value_mapper=get_value_mapper(self.app))
-        category_dict["repositories"] = self.app.repository_registry.viewable_repositories_and_suites_by_category.get(
-            category.name, 0
-        )
+        category_dict["repositories"] = category.active_repository_count()
         category_dict["url"] = web.url_for(
             controller="categories", action="show", id=self.app.security.encode_id(category.id)
         )

lib/tool_shed/repository_registry.py

@@ -6,6 +6,7 @@ from sqlalchemy import (
     or_,
     select,
 )
+from typing_extensions import Protocol
 
 import tool_shed.repository_types.util as rt_util
 from tool_shed.util import (
@@ -18,11 +19,77 @@ from tool_shed.webapp.model import (
     Repository,
     RepositoryMetadata,
 )
+from .structured_app import ToolShedApp
 
 log = logging.getLogger(__name__)
 
 
-class Registry:
+class RegistryInterface(Protocol):
+
+    # only used in legacy controllers - can drop when drop old tool shed webapp
+    def add_category_entry(self, category): ...
+
+    def add_entry(self, repository):
+        # used when creating a repository
+        # Used in legacy add_repository_registry_entry API endpoint - already deemed not worth pulling over to 2.0
+        # used in legacy undelete_repository admin controller
+        # used in legacy deprecate controller
+        ...
+
+    def edit_category_entry(self, old_name, new_name):
+        # used in legacy admin controller
+        ...
+
+    def is_valid(self, repository) -> bool:
+        # probably not used outside this class but also not hurting anything
+        ...
+
+    def remove_category_entry(self, category): ...
+
+    def remove_entry(self, repository): ...
+
+
+# stop gap to implement the same general interface as repository_registry but do nothing,
+# I don't think this stuff is needed - outside potentially old test cases?
+class NullRepositoryRegistry(RegistryInterface):
+
+    def __init__(self, app: ToolShedApp):
+        self.app = app
+
+        # all of these are only used by repository_grids - which I think the tool shed 2.0
+        # does not use at all - but they are part of the "public interface" consumed by
+        # the full registry.
+        self.certified_level_one_viewable_repositories_and_suites_by_category: dict = {}
+        self.certified_level_one_viewable_suites_by_category: dict = {}
+        self.viewable_repositories_and_suites_by_category: dict = {}
+        self.viewable_suites_by_category: dict = {}
+        self.viewable_valid_repositories_and_suites_by_category: dict = {}
+        self.viewable_valid_suites_by_category: dict = {}
+
+    def add_category_entry(self, category):
+        # only used in legacy controllers - can drop when drop old tool shed webapp
+        pass
+
+    def add_entry(self, repository):
+        # used when creating a repository, and maybe more?
+        pass
+
+    def edit_category_entry(self, old_name, new_name):
+        pass
+
+    def is_valid(self, repository) -> bool:
+        if repository and not repository.deleted and not repository.deprecated and repository.downloadable_revisions:
+            return True
+        return False
+
+    def remove_category_entry(self, category):
+        pass
+
+    def remove_entry(self, repository):
+        pass
+
+
+class Registry(RegistryInterface):
     def __init__(self, app):
         log.debug("Loading the repository registry...")
         self.app = app
@@ -32,17 +99,30 @@ class Registry:
         self.certified_level_one_suite_tuples = []
         # These category dictionaries contain entries where the key is the category and the value is the integer count
         # of viewable repositories within that category.
+
+        # only used internally to class and by repository_grids
         self.certified_level_one_viewable_repositories_and_suites_by_category = {}
+        # only used internally to class and by repository_grids
         self.certified_level_one_viewable_suites_by_category = {}
-        self.certified_level_two_repository_and_suite_tuples = []
-        self.certified_level_two_suite_tuples = []
-        self.certified_level_two_viewable_repositories_and_suites_by_category = {}
-        self.certified_level_two_viewable_suites_by_category = {}
+
+        # not even used in legacy shed code...
+        # self.certified_level_two_repository_and_suite_tuples = []
+        # self.certified_level_two_suite_tuples = []
+        # self.certified_level_two_viewable_repositories_and_suites_by_category = {}
+        # self.certified_level_two_viewable_suites_by_category = {}
+
+        # only used internally to class
         self.repository_and_suite_tuples = []
+        # only used internally to class
         self.suite_tuples = []
+
+        # only used internally to class and by repository_grids
         self.viewable_repositories_and_suites_by_category = {}
+        # only used internally to class and by repository_grids
         self.viewable_suites_by_category = {}
+        # only used internally to class and by repository_grids
         self.viewable_valid_repositories_and_suites_by_category = {}
+        # only used internally to class and by repository_grids
         self.viewable_valid_suites_by_category = {}
         self.load()
 
@@ -152,6 +232,7 @@ class Registry:
             self.certified_level_one_viewable_suites_by_category[new_name] = 0
 
     def get_certified_level_one_clause_list(self):
+        # only used internally to class
         clause_list = []
         for repository in get_repositories(self.sa_session):
             certified_level_one_tuple = self.get_certified_level_one_tuple(repository)
@@ -169,6 +250,7 @@ class Registry:
         """
         Return True if the latest installable changeset_revision of the received repository is level one certified.
         """
+        # only used internally to class
         if repository is None:
             return (None, False)
         if repository.deleted or repository.deprecated:
@@ -190,6 +272,7 @@ class Registry:
             return (None, False)
 
     def is_level_one_certified(self, repository_metadata):
+        # only used internally to class
         if repository_metadata:
             repository = repository_metadata.repository
             if repository:
@@ -206,12 +289,13 @@ class Registry:
                     return tuple in self.certified_level_one_repository_and_suite_tuples
         return False
 
-    def is_valid(self, repository):
+    def is_valid(self, repository) -> bool:
         if repository and not repository.deleted and not repository.deprecated and repository.downloadable_revisions:
             return True
         return False
 
     def load_certified_level_one_repository_and_suite_tuple(self, repository):
+        # only used internally to class
         # The received repository has been determined to be level one certified.
         name = str(repository.name)
         owner = str(repository.user.username)
@@ -226,6 +310,7 @@ class Registry:
                     self.certified_level_one_repository_and_suite_tuples.append(certified_level_one_tuple)
 
     def load_repository_and_suite_tuple(self, repository):
+        # only used internally to class
         name = str(repository.name)
         owner = str(repository.user.username)
         for repository_metadata in repository.metadata_revisions:
@@ -238,6 +323,7 @@ class Registry:
                     self.suite_tuples.append(tuple)
 
     def load_repository_and_suite_tuples(self):
+        # only used internally to class
         # Load self.certified_level_one_repository_and_suite_tuples and self.certified_level_one_suite_tuples.
         clauses = self.get_certified_level_one_clause_list()
         for repository in get_certified_repositories_with_user(self.sa_session, clauses, model.User):
@@ -247,11 +333,12 @@ class Registry:
             self.load_repository_and_suite_tuple(repository)
 
     def load_viewable_repositories_and_suites_by_category(self):
+        # only used internally to class
         # Clear all dictionaries just in case they were previously loaded.
         self.certified_level_one_viewable_repositories_and_suites_by_category = {}
         self.certified_level_one_viewable_suites_by_category = {}
-        self.certified_level_two_viewable_repositories_and_suites_by_category = {}
-        self.certified_level_two_viewable_suites_by_category = {}
+        # self.certified_level_two_viewable_repositories_and_suites_by_category = {}
+        # self.certified_level_two_viewable_suites_by_category = {}
         self.viewable_repositories_and_suites_by_category = {}
         self.viewable_suites_by_category = {}
         self.viewable_valid_repositories_and_suites_by_category = {}
@@ -363,6 +450,7 @@ class Registry:
 
     @property
     def sa_session(self):
+        # only used internally to class
         return self.app.model.session
 
     def unload_certified_level_one_repository_and_suite_tuple(self, repository):

lib/tool_shed/structured_app.py

@@ -4,7 +4,7 @@ from galaxy.structured_app import BasicSharedApp
 
 if TYPE_CHECKING:
     from tool_shed.managers.model_cache import ModelCache
-    from tool_shed.repository_registry import Registry as RepositoryRegistry
+    from tool_shed.repository_registry import RegistryInterface
     from tool_shed.repository_types.registry import Registry as RepositoryTypesRegistry
     from tool_shed.util.hgweb_config import HgWebConfigManager
     from tool_shed.webapp.model import mapping
@@ -14,7 +14,7 @@ if TYPE_CHECKING:
 class ToolShedApp(BasicSharedApp):
     repository_types_registry: "RepositoryTypesRegistry"
     model: "mapping.ToolShedModelMapping"
-    repository_registry: "RepositoryRegistry"
+    repository_registry: "RegistryInterface"
     hgweb_config_manager: "HgWebConfigManager"
     security_agent: "CommunityRBACAgent"
     model_cache: "ModelCache"

lib/tool_shed/webapp/app.py

@@ -108,7 +108,10 @@ class UniverseApplication(ToolShedApp, SentryClientMixin, HaltableContainer):
         self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
         self.hgweb_config_manager.hgweb_repo_prefix = self.config.hgweb_repo_prefix
         # Initialize the repository registry.
-        self.repository_registry = tool_shed.repository_registry.Registry(self)
+        if config.SHED_API_VERSION != "v2":
+            self.repository_registry = tool_shed.repository_registry.Registry(self)
+        else:
+            self.repository_registry = tool_shed.repository_registry.NullRepositoryRegistry(self)
         # Configure Sentry client if configured
         self.configure_sentry_client()
         #  used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.

lib/tool_shed/webapp/buildapp.py

@@ -26,8 +26,7 @@ from galaxy.webapps.base.webapp import (
     GalaxyWebTransaction,
 )
 from galaxy.webapps.util import wrap_if_allowed
-
-SHED_API_VERSION = os.environ.get("TOOL_SHED_API_VERSION", "v1")
+from .config import SHED_API_VERSION
 
 log = logging.getLogger(__name__)
 

lib/tool_shed/webapp/config.py

@@ -27,6 +27,7 @@ from galaxy.version import (
 log = logging.getLogger(__name__)
 
 TOOLSHED_APP_NAME = "tool_shed"
+SHED_API_VERSION = os.environ.get("TOOL_SHED_API_VERSION", "v1")
 
 
 class ToolShedAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):

lib/tool_shed/webapp/fast_app.py

@@ -166,7 +166,7 @@ def initialize_fast_app(gx_webapp, tool_shed_app):
     app = get_fastapi_instance()
     add_exception_handler(app)
     add_request_id_middleware(app)
-    from .buildapp import SHED_API_VERSION
+    from .config import SHED_API_VERSION
 
     def mount_static(directory: Path):
         name = directory.name

lib/tool_shed/webapp/model/__init__.py

@@ -28,6 +28,7 @@ from sqlalchemy import (
     not_,
     String,
     Table,
+    text,
     TEXT,
     true,
     UniqueConstraint,
@@ -35,6 +36,7 @@ from sqlalchemy import (
 from sqlalchemy.orm import (
     Mapped,
     mapped_column,
+    object_session,
     registry,
     relationship,
 )
@@ -618,6 +620,22 @@ class Category(Base, Dictifiable):
     dict_collection_visible_keys = ["id", "name", "description", "deleted"]
     dict_element_visible_keys = ["id", "name", "description", "deleted"]
 
+    def active_repository_count(self, session=None) -> int:
+        statement = """
+SELECT count(*) as count
+FROM repository r
+INNER JOIN repository_category_association rca on rca.repository_id = r.id
+WHERE
+    rca.category_id = :category_id
+    AND r.private = false
+    AND r.deleted = false
+    and r.deprecated = false
+"""
+        if session is None:
+            session = object_session(self)
+        params = {"category_id": self.id}
+        return session.execute(text(statement), params).scalar()
+
     def __init__(self, deleted=False, **kwd):
         super().__init__(**kwd)
         self.deleted = deleted

test/unit/tool_shed/_util.py

@@ -33,6 +33,7 @@ from tool_shed.webapp.model import (
     Category,
     mapping,
     Repository,
+    RepositoryCategoryAssociation,
     User,
 )
 from tool_shed_client.schema import CreateCategoryRequest
@@ -195,3 +196,12 @@ def create_category(provides_repositories: ProvidesRepositoriesContext, create:
 
     request = CreateCategoryRequest(**create)
     return CategoryManager(provides_repositories.app).create(provides_repositories, request)
+
+
+def attach_category(provides_repositories: ProvidesRepositoriesContext, repository: Repository, category: Category):
+    assoc = RepositoryCategoryAssociation(
+        repository=repository,
+        category=category,
+    )
+    provides_repositories.sa_session.add(assoc)
+    provides_repositories.sa_session.flush()

test/unit/tool_shed/test_graphql.py

@@ -12,12 +12,9 @@ from tool_shed.context import (
     ProvidesUserContext,
 )
 from tool_shed.webapp.graphql.schema import schema
-from tool_shed.webapp.model import (
-    Category,
-    Repository,
-    RepositoryCategoryAssociation,
-)
+from tool_shed.webapp.model import Repository
 from ._util import (
+    attach_category,
     create_category,
     repository_fixture,
     upload_directories_to_repository,
@@ -110,15 +107,6 @@ def test_simple_repositories(provides_repositories: ProvidesRepositoriesContext,
     assert new_repository.name in repository_names
 
 
-def attach_category(provides_repositories: ProvidesRepositoriesContext, repository: Repository, category: Category):
-    assoc = RepositoryCategoryAssociation(
-        repository=repository,
-        category=category,
-    )
-    provides_repositories.sa_session.add(assoc)
-    provides_repositories.sa_session.flush()
-
-
 def test_relay_repos_by_category(provides_repositories: ProvidesRepositoriesContext, new_repository: Repository):
     name = new_repository.name
     category = create_category(provides_repositories, {"name": "test_graphql_relay_categories_1"})

test/unit/tool_shed/test_repository_utils.py

@@ -5,6 +5,8 @@ from tool_shed.webapp.model import (
     User,
 )
 from ._util import (
+    attach_category,
+    create_category,
     repository_fixture,
     TEST_DATA_FILES,
     TestToolShedApp,
@@ -83,6 +85,27 @@ def test_upload_dry_run_ok(provides_repositories: ProvidesRepositoriesContext, n
     assert old_tip == new_tip
 
 
+def test_category_count(provides_repositories: ProvidesRepositoriesContext, new_repository: Repository):
+    category = create_category(provides_repositories, {"name": "test_category_count_1"})
+    attach_category(provides_repositories, new_repository, category)
+
+    category = new_repository.categories[0].category
+    assert category.active_repository_count() == 1
+
+    tar_resource = TEST_DATA_FILES.joinpath("column_maker/column_maker.tar")
+    upload_ok, *_ = upload_tar(
+        provides_repositories,
+        new_repository.user.username,
+        new_repository,
+        tar_resource,
+        commit_message="Commit Message",
+    )
+    assert upload_ok
+
+    category = new_repository.categories[0].category
+    assert category.active_repository_count() == 1
+
+
 def test_upload_dry_run_failed(provides_repositories: ProvidesRepositoriesContext, new_repository: Repository):
     tar_resource = TEST_DATA_FILES.joinpath("safetar_with_symlink.tar")
     upload_ok, message, _, _, _, _ = upload_tar(