Standalone implementation of tool shed client...

.github/workflows/toolshed.yaml

@@ -21,6 +21,7 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.7']
+        test-install-client: ['standalone', 'galaxy_api']
     services:
       postgres:
         image: postgres:13
@@ -54,9 +55,11 @@ jobs:
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-toolshed
       - name: Run tests
         run: './run_tests.sh -toolshed'
+        env:
+          TOOL_SHED_TEST_INSTALL_CLIENT: ${{ matrix.test-install-client }}
         working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v3
         if: failure()
         with:
-          name: Toolshed test results (${{ matrix.python-version }})
+          name: Toolshed test results (${{ matrix.python-version }}, ${{ matrix.test-install-client }})
           path: 'galaxy root/run_toolshed_tests.html'

lib/galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py

@@ -15,6 +15,7 @@
     urlopen,
 )
 
+from galaxy.tool_shed.galaxy_install import installed_repository_manager
 from galaxy.tool_shed.galaxy_install.tools import tool_panel_manager
 from galaxy.tool_shed.util import repository_util
 from galaxy.tool_shed.util.container_util import get_components_from_key
@@ -263,7 +264,8 @@ def create_repository_dependency_objects(
                                 log.info(
                                     f"Reactivating deactivated tool_shed_repository '{str(repository_db_record.name)}'."
                                 )
-                                self.app.installed_repository_manager.activate_repository(repository_db_record)
+                                irm = installed_repository_manager.InstalledRepositoryManager(self.app)
+                                irm.activate_repository(repository_db_record)
                                 # No additional updates to the database record are necessary.
                                 can_update_db_record = False
                             elif repository_db_record.status not in [

lib/galaxy/tool_shed/util/dependency_display.py

@@ -2,6 +2,7 @@
 import os
 
 from galaxy import util
+from galaxy.tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
 from galaxy.tool_shed.util import utility_container_manager
 from galaxy.util.tool_shed.common_util import parse_repository_dependency_tuple
 
@@ -197,11 +198,12 @@ def populate_containers_dict_from_repository_metadata(self, repository):
         """
         metadata = repository.metadata_
         if metadata:
+            irm = InstalledRepositoryManager(self.app)
             # Handle repository dependencies.
             (
                 installed_repository_dependencies,
                 missing_repository_dependencies,
-            ) = self.app.installed_repository_manager.get_installed_and_missing_repository_dependencies(repository)
+            ) = irm.get_installed_and_missing_repository_dependencies(repository)
             # Handle the current repository's tool dependencies.
             repository_tool_dependencies = metadata.get("tool_dependencies", None)
             # Make sure to display missing tool dependencies as well.
@@ -290,3 +292,20 @@ def build_repository_containers(
         except Exception as e:
             log.debug(f"Exception in build_repository_containers: {str(e)}")
         return containers_dict
+
+
+def build_manage_repository_dict(app, status, repository):
+    dd = DependencyDisplayer(app)
+    containers_dict = dd.populate_containers_dict_from_repository_metadata(
+        repository=repository,
+    )
+    management_dict = {
+        "status": status,
+    }
+    missing_repo_dependencies = containers_dict.get("missing_repository_dependencies", None)
+    if missing_repo_dependencies:
+        management_dict["missing_repository_dependencies"] = missing_repo_dependencies.to_dict()
+    repository_dependencies = containers_dict.get("repository_dependencies", None)
+    if repository_dependencies:
+        management_dict["repository_dependencies"] = repository_dependencies.to_dict()
+    return management_dict

lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

@@ -153,17 +153,4 @@ def _manage_repository_json(self, trans, **kwd):
                 trans.install_model.context.add(repository)
                 trans.install_model.context.flush()
             message = "The repository information has been updated."
-        dd = dependency_display.DependencyDisplayer(trans.app)
-        containers_dict = dd.populate_containers_dict_from_repository_metadata(
-            repository=repository,
-        )
-        management_dict = {
-            "status": status,
-        }
-        missing_repo_dependencies = containers_dict.get("missing_repository_dependencies", None)
-        if missing_repo_dependencies:
-            management_dict["missing_repository_dependencies"] = missing_repo_dependencies.to_dict()
-        repository_dependencies = containers_dict.get("repository_dependencies", None)
-        if repository_dependencies:
-            management_dict["repository_dependencies"] = repository_dependencies.to_dict()
-        return management_dict
+        return dependency_display.build_manage_repository_dict(trans.app, status, repository)

lib/tool_shed/test/base/test_db_util.py

@@ -1,5 +1,8 @@
 import logging
-from typing import Optional
+from typing import (
+    List,
+    Optional,
+)
 
 from sqlalchemy import (
     and_,
@@ -38,22 +41,19 @@ def get_all_repositories():
     return sa_session.query(model.Repository).all()
 
 
-def get_all_installed_repositories(actually_installed=False):
-    if actually_installed:
-        return (
-            install_session.query(galaxy.model.tool_shed_install.ToolShedRepository)
-            .filter(
-                and_(
-                    galaxy.model.tool_shed_install.ToolShedRepository.table.c.deleted == false(),
-                    galaxy.model.tool_shed_install.ToolShedRepository.table.c.uninstalled == false(),
-                    galaxy.model.tool_shed_install.ToolShedRepository.table.c.status
-                    == galaxy.model.tool_shed_install.ToolShedRepository.installation_status.INSTALLED,
-                )
+def get_all_installed_repositories(session=install_session) -> List[galaxy.model.tool_shed_install.ToolShedRepository]:
+    return list(
+        session.query(galaxy.model.tool_shed_install.ToolShedRepository)
+        .filter(
+            and_(
+                galaxy.model.tool_shed_install.ToolShedRepository.table.c.deleted == false(),
+                galaxy.model.tool_shed_install.ToolShedRepository.table.c.uninstalled == false(),
+                galaxy.model.tool_shed_install.ToolShedRepository.table.c.status
+                == galaxy.model.tool_shed_install.ToolShedRepository.installation_status.INSTALLED,
             )
-            .all()
         )
-    else:
-        return install_session.query(galaxy.model.tool_shed_install.ToolShedRepository).all()
+        .all()
+    )
 
 
 def get_galaxy_repository_by_name_owner_changeset_revision(repository_name, owner, changeset_revision):
@@ -78,8 +78,8 @@ def get_installed_repository_by_id(repository_id):
     )
 
 
-def get_installed_repository_by_name_owner(repository_name, owner, return_multiple=False):
-    query = install_session.query(galaxy.model.tool_shed_install.ToolShedRepository).filter(
+def get_installed_repository_by_name_owner(repository_name, owner, return_multiple=False, session=install_session):
+    query = session.query(galaxy.model.tool_shed_install.ToolShedRepository).filter(
         and_(
             galaxy.model.tool_shed_install.ToolShedRepository.table.c.name == repository_name,
             galaxy.model.tool_shed_install.ToolShedRepository.table.c.owner == owner,