From e2c740337d94bdd06ad6df223a05560624d6e776 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Tue, 19 Oct 2021 17:30:39 -0400
Subject: [PATCH 01/23] Rename mapping test, add install_model_mapping test

---
 test/unit/data/model/test_install_model_mapping.py              | 0
 test/unit/data/model/{test_mapping.py => test_model_mapping.py} | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 test/unit/data/model/test_install_model_mapping.py
 rename test/unit/data/model/{test_mapping.py => test_model_mapping.py} (100%)

diff --git a/test/unit/data/model/test_install_model_mapping.py b/test/unit/data/model/test_install_model_mapping.py
new file mode 100644
index 000000000000..e69de29bb2d1
diff --git a/test/unit/data/model/test_mapping.py b/test/unit/data/model/test_model_mapping.py
similarity index 100%
rename from test/unit/data/model/test_mapping.py
rename to test/unit/data/model/test_model_mapping.py

From fb7f71a39668e48867b069df525c7d5caa584d83 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Tue, 19 Oct 2021 21:45:14 -0400
Subject: [PATCH 02/23] Add unit tests for install_model mapping

---
 .../data/model/test_install_model_mapping.py  | 394 ++++++++++++++++++
 1 file changed, 394 insertions(+)

diff --git a/test/unit/data/model/test_install_model_mapping.py b/test/unit/data/model/test_install_model_mapping.py
index e69de29bb2d1..844e8f8f682a 100644
--- a/test/unit/data/model/test_install_model_mapping.py
+++ b/test/unit/data/model/test_install_model_mapping.py
@@ -0,0 +1,394 @@
+from contextlib import contextmanager
+from datetime import datetime, timedelta
+
+import pytest
+from sqlalchemy import (
+    delete,
+    select,
+)
+
+import galaxy.model.tool_shed_install.mapping as mapping
+
+
+class BaseTest:
+    @pytest.fixture
+    def cls_(self, model):
+        """
+        Return class under test.
+        Assumptions: if the class under test is Foo, then the class grouping
+        the tests should be a subclass of BaseTest, named TestFoo.
+        """
+        prefix = len('Test')
+        class_name = self.__class__.__name__[prefix:]
+        return getattr(model, class_name)
+
+
+class TestToolShedRepository(BaseTest):
+
+    def test_table(self, cls_):
+        assert cls_.table.name == 'tool_shed_repository'
+        # assert cls_.__tablename__ == 'tool_shed_repository'  # TODO
+
+    def test_columns(self, session, cls_, repository):
+        create_time = datetime.now()
+        update_time = create_time + timedelta(hours=1)
+        tool_shed = 'a'
+        name = 'b'
+        description = 'c'
+        owner = 'd'
+        installed_changeset_revision = 'e'
+        changeset_revision = 'f'
+        ctx_rev = 'g'
+        metadata = 'h'
+        includes_datatypes = True
+        tool_shed_status = 'i'
+        deleted = True
+        uninstalled = True
+        dist_to_shed = True
+        status = 'j'
+        error_message = 'k'
+
+        obj = cls_()
+        obj.create_time = create_time
+        obj.update_time = update_time
+        obj.tool_shed = tool_shed
+        obj.name = name
+        obj.description = description
+        obj.owner = owner
+        obj.installed_changeset_revision = installed_changeset_revision
+        obj.changeset_revision = changeset_revision
+        obj.ctx_rev = ctx_rev
+        obj.metadata = metadata
+        obj.includes_datatypes = includes_datatypes
+        obj.tool_shed_status = tool_shed_status
+        obj.deleted = deleted
+        obj.uninstalled = uninstalled
+        obj.dist_to_shed = dist_to_shed
+        obj.status = status
+        obj.error_message = error_message
+
+        with dbcleanup(session, obj) as obj_id:
+            stored_obj = get_stored_obj(session, cls_, obj_id)
+            assert stored_obj.id == obj_id
+            assert stored_obj.create_time == create_time
+            assert stored_obj.update_time == update_time
+            assert stored_obj.tool_shed == tool_shed
+            assert stored_obj.name == name
+            assert stored_obj.description == description
+            assert stored_obj.owner == owner
+            assert stored_obj.installed_changeset_revision == installed_changeset_revision
+            assert stored_obj.changeset_revision == changeset_revision
+            assert stored_obj.ctx_rev == ctx_rev
+            assert stored_obj.metadata == metadata
+            assert stored_obj.includes_datatypes == includes_datatypes
+            assert stored_obj.tool_shed_status == tool_shed_status
+            assert stored_obj.deleted == deleted
+            assert stored_obj.uninstalled == uninstalled
+            assert stored_obj.dist_to_shed == dist_to_shed
+            assert stored_obj.status == status
+            assert stored_obj.error_message == error_message
+
+    def test_relationships(
+        self,
+        session, cls_,
+        repository,
+        tool_version,
+        tool_dependency,
+        repository_repository_dependency_association,
+    ):
+        obj = cls_()
+        obj.tool_versions.append(tool_version)
+        obj.tool_dependencies.append(tool_dependency)
+        obj.required_repositories.append(repository_repository_dependency_association)
+
+        with dbcleanup(session, obj) as obj_id:
+            stored_obj = get_stored_obj(session, cls_, obj_id)
+            assert stored_obj.tool_versions == [tool_version]
+            assert stored_obj.tool_dependencies == [tool_dependency]
+            assert stored_obj.required_repositories == [repository_repository_dependency_association]
+
+
+class TestRepositoryRepositoryDependencyAssociation(BaseTest):
+
+    def test_table(self, cls_):
+        assert cls_.table.name == 'repository_repository_dependency_association'
+        # assert cls_.__tablename__ == 'repository_dependency'  # TODO
+
+    def test_columns(self, session, cls_, repository, repository_dependency):
+        create_time = datetime.now()
+        update_time = create_time + timedelta(hours=1)
+        obj = cls_()
+        obj.create_time = create_time
+        obj.update_time = update_time
+        obj.repository = repository
+        obj.repository_dependency = repository_dependency
+
+        with dbcleanup(session, obj) as obj_id:
+            stored_obj = get_stored_obj(session, cls_, obj_id)
+            assert stored_obj.id == obj_id
+            assert stored_obj.create_time == create_time
+            assert stored_obj.update_time == update_time
+            assert stored_obj.tool_shed_repository_id == repository.id
+            assert stored_obj.repository_dependency_id == repository_dependency.id
+
+    def test_relationships(self, session, cls_, repository, repository_dependency):
+        obj = cls_()
+        obj.repository = repository
+        obj.repository_dependency = repository_dependency
+
+        with dbcleanup(session, obj) as obj_id:
+            stored_obj = get_stored_obj(session, cls_, obj_id)
+            assert stored_obj.repository.id == repository.id
+            assert stored_obj.repository_dependency.id == repository_dependency.id
+
+
+class TestRepositoryDependency(BaseTest):
+
+    def test_table(self, cls_):
+        assert cls_.table.name == 'repository_dependency'
+        # assert cls_.__tablename__ == 'repository_dependency'  # TODO
+
+    def test_columns(self, session, cls_, repository):
+        create_time = datetime.now()
+        update_time = create_time + timedelta(hours=1)
+        obj = cls_()
+        obj.create_time = create_time
+        obj.update_time = update_time
+        obj.repository = repository
+
+        with dbcleanup(session, obj) as obj_id:
+            stored_obj = get_stored_obj(session, cls_, obj_id)
+            assert stored_obj.id == obj_id
+            assert stored_obj.create_time == create_time
+            assert stored_obj.update_time == update_time
+            assert stored_obj.tool_shed_repository_id == repository.id
+
+    def test_relationships(self, session, cls_, repository):
+        obj = cls_()
+        obj.repository = repository
+
+        with dbcleanup(session, obj) as obj_id:
+            stored_obj = get_stored_obj(session, cls_, obj_id)
+            assert stored_obj.repository.id == repository.id
+
+
+class TestToolDependency(BaseTest):
+
+    def test_table(self, cls_):
+        assert cls_.table.name == 'tool_dependency'
+        # assert cls_.__tablename__ == 'tool_dependency'  # TODO
+
+    def test_columns(self, session, cls_, repository):
+        create_time = datetime.now()
+        update_time = create_time + timedelta(hours=1)
+        name, version, type, status, error_message = 'a', 'b', 'c', 'd', 'e'
+        obj = cls_()
+        obj.create_time = create_time
+        obj.update_time = update_time
+        obj.tool_shed_repository_id = repository.id
+        obj.name = name
+        obj.version = version
+        obj.type = type
+        obj.status = status
+        obj.error_message = error_message
+
+        with dbcleanup(session, obj) as obj_id:
+            stored_obj = get_stored_obj(session, cls_, obj_id)
+            assert stored_obj.id == obj_id
+            assert stored_obj.create_time == create_time
+            assert stored_obj.update_time == update_time
+            assert stored_obj.tool_shed_repository_id == repository.id
+            assert stored_obj.name == name
+            assert stored_obj.version == version
+            assert stored_obj.type == type
+            assert stored_obj.status == status
+            assert stored_obj.error_message == error_message
+
+    def test_relationships(self, session, cls_, repository):
+        obj = cls_()
+        obj.tool_shed_repository = repository
+        obj.status = 'a'
+
+        with dbcleanup(session, obj) as obj_id:
+            stored_obj = get_stored_obj(session, cls_, obj_id)
+            assert stored_obj.tool_shed_repository.id == repository.id
+
+
+class TestToolVersion(BaseTest):
+
+    def test_table(self, cls_):
+        assert cls_.table.name == 'tool_version'
+        # assert cls_.__tablename__ == 'tool_version'  # TODO
+
+    def test_columns(self, session, cls_, repository):
+        create_time = datetime.now()
+        update_time = create_time + timedelta(hours=1)
+        tool_id = 'a'
+        obj = cls_()
+        obj.create_time = create_time
+        obj.update_time = update_time
+        obj.tool_id = tool_id
+        obj.tool_shed_repository = repository
+
+        with dbcleanup(session, obj) as obj_id:
+            stored_obj = get_stored_obj(session, cls_, obj_id)
+            assert stored_obj.id == obj_id
+            assert stored_obj.create_time == create_time
+            assert stored_obj.update_time == update_time
+            assert stored_obj.tool_id == tool_id
+            assert stored_obj.tool_shed_repository_id == repository.id
+
+    def test_relationships(self, session, cls_, repository):
+        obj = cls_()
+        obj.tool_shed_repository = repository
+        # TODO
+        # parent_tool_association
+        # child_tool_association
+
+        with dbcleanup(session, obj) as obj_id:
+            stored_obj = get_stored_obj(session, cls_, obj_id)
+            assert stored_obj.tool_shed_repository.id == repository.id
+
+
+class TestToolVersionAssociation(BaseTest):
+
+    def test_table(self, cls_):
+        assert cls_.table.name == 'tool_version_association'
+        # assert cls_.__tablename__ == 'tool_version_association'  # TODO
+
+    def test_columns(self, session, cls_, tool_version_factory):
+        tool_version = tool_version_factory()
+        parent_tool_version = tool_version_factory()
+
+        session.add(tool_version)
+        session.add(parent_tool_version)
+        session.flush()
+
+        # TODO: why are these not mapped as relationships?
+        obj = cls_()
+        obj.tool_id = tool_version.id
+        obj.parent_id = parent_tool_version.id
+
+        with dbcleanup(session, obj) as obj_id:
+            stored_obj = get_stored_obj(session, cls_, obj_id)
+            assert stored_obj.id == obj_id
+            assert stored_obj.tool_id == tool_version.id
+            assert stored_obj.parent_id == parent_tool_version.id
+
+
+# Misc. helper fixtures.
+
+@pytest.fixture(scope='module')
+def model():
+    db_uri = 'sqlite:///:memory:'
+    return mapping.init(db_uri, create_tables=True)
+
+
+@pytest.fixture
+def session(model):
+    Session = model.session
+    yield Session()
+    Session.remove()  # Ensures we get a new session for each test
+
+
+# Fixtures yielding persisted instances of models, deleted from the database on test exit.
+
+@pytest.fixture
+def repository(model, session):
+    instance = model.ToolShedRepository()
+    yield from dbcleanup_wrapper(session, instance)
+
+
+@pytest.fixture
+def repository_repository_dependency_association(model, session):
+    instance = model.RepositoryRepositoryDependencyAssociation()
+    yield from dbcleanup_wrapper(session, instance)
+
+
+@pytest.fixture
+def repository_dependency(model, session, repository):
+    instance = model.RepositoryDependency()
+    instance.repository = repository
+    yield from dbcleanup_wrapper(session, instance)
+
+
+@pytest.fixture
+def tool_dependency(model, session, repository):
+    instance = model.ToolDependency()
+    instance.tool_shed_repository = repository
+    instance.status = 'a'
+    yield from dbcleanup_wrapper(session, instance)
+
+
+@pytest.fixture
+def tool_version(model, session):
+    instance = model.ToolVersion()
+    yield from dbcleanup_wrapper(session, instance)
+
+
+@pytest.fixture
+def tool_version_factory(model):
+    def make_instance(*args, **kwds):
+        return model.ToolVersion(*args, **kwds)
+    return make_instance
+
+
+# Test utilities
+
+def dbcleanup_wrapper(session, obj, where_clause=None):
+    with dbcleanup(session, obj, where_clause):
+        yield obj
+
+
+@contextmanager
+def dbcleanup(session, obj, where_clause=None):
+    """
+    Use the session to store obj in database; delete from database on exit, bypassing the session.
+
+    If obj does not have an id field, a SQLAlchemy WHERE clause should be provided to construct
+    a custom select statement.
+    """
+    return_id = where_clause is None
+
+    try:
+        obj_id = persist(session, obj, return_id)
+        yield obj_id
+    finally:
+        # table = obj.__table__  # TODO
+        table = obj.table
+        if where_clause is None:
+            where_clause = _get_default_where_clause(type(obj), obj_id)
+        stmt = delete(table).where(where_clause)
+        session.execute(stmt)
+
+
+def persist(session, obj, return_id=True):
+    """
+    Use the session to store obj in database, then remove obj from session,
+    so that on a subsequent load from the database we get a clean instance.
+    """
+    session.add(obj)
+    session.flush()
+    obj_id = obj.id if return_id else None  # save this before obj is expunged
+    session.expunge(obj)
+    return obj_id
+
+
+def get_stored_obj(session, cls, obj_id=None, where_clause=None, unique=False):
+    # Either obj_id or where_clause must be provided, but not both
+    assert bool(obj_id) ^ (where_clause is not None)
+    if where_clause is None:
+        where_clause = _get_default_where_clause(cls, obj_id)
+    stmt = select(cls).where(where_clause)
+    result = session.execute(stmt)
+    # unique() is required if result contains joint eager loads against collections
+    # https://gerrit.sqlalchemy.org/c/sqlalchemy/sqlalchemy/+/2253
+    if unique:
+        result = result.unique()
+    return result.scalar_one()
+
+
+def _get_default_where_clause(cls, obj_id):
+    # where_clause = cls.__table__.c.id == obj_id  # TODO
+    where_clause = cls.table.c.id == obj_id
+    return where_clause

From 6f45f262aaf7983d0ae539994520ec13d178d468 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Tue, 19 Oct 2021 22:10:27 -0400
Subject: [PATCH 03/23] Setup install_model for remapping

---
 .../model/tool_shed_install/__init__.py       |  3 +++
 lib/galaxy/model/tool_shed_install/mapping.py | 21 ++++++++-----------
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py
index d878682842ee..f0bc3fe373c5 100644
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -3,6 +3,8 @@
 from enum import Enum
 from typing import TYPE_CHECKING
 
+from sqlalchemy.orm import registry
+
 from galaxy.util import asbool
 from galaxy.util.bunch import Bunch
 from galaxy.util.dictifiable import Dictifiable
@@ -10,6 +12,7 @@
 
 log = logging.getLogger(__name__)
 
+mapper_registry = registry()
 
 if TYPE_CHECKING:
     from sqlalchemy.schema import Table
diff --git a/lib/galaxy/model/tool_shed_install/mapping.py b/lib/galaxy/model/tool_shed_install/mapping.py
index 8dd657feb158..6b8ee051fbd0 100644
--- a/lib/galaxy/model/tool_shed_install/mapping.py
+++ b/lib/galaxy/model/tool_shed_install/mapping.py
@@ -4,15 +4,11 @@
     DateTime,
     ForeignKey,
     Integer,
-    MetaData,
     String,
     Table,
     TEXT
 )
-from sqlalchemy.orm import (
-    mapper,
-    relation
-)
+from sqlalchemy.orm import relation
 
 from galaxy.model import tool_shed_install as install_model
 from galaxy.model.base import ModelMapping
@@ -22,8 +18,9 @@
 )
 from galaxy.model.orm.engine_factory import build_engine
 from galaxy.model.orm.now import now
+from galaxy.model.tool_shed_install import mapper_registry
 
-metadata = MetaData()
+metadata = mapper_registry.metadata
 
 install_model.ToolShedRepository.table = Table("tool_shed_repository", metadata,
                                                Column("id", Integer, primary_key=True),
@@ -86,7 +83,7 @@
                                          Column("repository_path", TEXT),
                                          Column("version", Integer))
 
-mapper(install_model.ToolShedRepository, install_model.ToolShedRepository.table,
+mapper_registry.map_imperatively(install_model.ToolShedRepository, install_model.ToolShedRepository.table,
        properties=dict(tool_versions=relation(install_model.ToolVersion,
                                               primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.ToolVersion.table.c.tool_shed_repository_id),
                                               backref='tool_shed_repository'),
@@ -97,26 +94,26 @@
                        required_repositories=relation(install_model.RepositoryRepositoryDependencyAssociation,
                                                       primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.RepositoryRepositoryDependencyAssociation.table.c.tool_shed_repository_id))))
 
-mapper(install_model.RepositoryRepositoryDependencyAssociation, install_model.RepositoryRepositoryDependencyAssociation.table,
+mapper_registry.map_imperatively(install_model.RepositoryRepositoryDependencyAssociation, install_model.RepositoryRepositoryDependencyAssociation.table,
        properties=dict(repository=relation(install_model.ToolShedRepository,
                                            primaryjoin=(install_model.RepositoryRepositoryDependencyAssociation.table.c.tool_shed_repository_id == install_model.ToolShedRepository.table.c.id)),
                        repository_dependency=relation(install_model.RepositoryDependency,
                                                       primaryjoin=(install_model.RepositoryRepositoryDependencyAssociation.table.c.repository_dependency_id == install_model.RepositoryDependency.table.c.id))))
 
-mapper(install_model.RepositoryDependency, install_model.RepositoryDependency.table,
+mapper_registry.map_imperatively(install_model.RepositoryDependency, install_model.RepositoryDependency.table,
        properties=dict(repository=relation(install_model.ToolShedRepository,
                                            primaryjoin=(install_model.RepositoryDependency.table.c.tool_shed_repository_id == install_model.ToolShedRepository.table.c.id))))
 
-mapper(install_model.ToolDependency, install_model.ToolDependency.table)
+mapper_registry.map_imperatively(install_model.ToolDependency, install_model.ToolDependency.table)
 
-mapper(install_model.ToolVersion, install_model.ToolVersion.table,
+mapper_registry.map_imperatively(install_model.ToolVersion, install_model.ToolVersion.table,
        properties=dict(
            parent_tool_association=relation(install_model.ToolVersionAssociation,
                                             primaryjoin=(install_model.ToolVersion.table.c.id == install_model.ToolVersionAssociation.table.c.tool_id)),
            child_tool_association=relation(install_model.ToolVersionAssociation,
                                            primaryjoin=(install_model.ToolVersion.table.c.id == install_model.ToolVersionAssociation.table.c.parent_id))))
 
-mapper(install_model.ToolVersionAssociation, install_model.ToolVersionAssociation.table)
+mapper_registry.map_imperatively(install_model.ToolVersionAssociation, install_model.ToolVersionAssociation.table)
 
 
 def init(url, engine_options=None, create_tables=False):

From 29e188597539e3205904857faa59998fa2211bc8 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 12:25:07 -0400
Subject: [PATCH 04/23] Add nonstandard test for ToolVersion relationships

---
 .../data/model/test_install_model_mapping.py  | 55 ++++++++++++++++---
 1 file changed, 48 insertions(+), 7 deletions(-)

diff --git a/test/unit/data/model/test_install_model_mapping.py b/test/unit/data/model/test_install_model_mapping.py
index 844e8f8f682a..2e0898a8db70 100644
--- a/test/unit/data/model/test_install_model_mapping.py
+++ b/test/unit/data/model/test_install_model_mapping.py
@@ -238,16 +238,34 @@ def test_columns(self, session, cls_, repository):
             assert stored_obj.tool_id == tool_id
             assert stored_obj.tool_shed_repository_id == repository.id
 
-    def test_relationships(self, session, cls_, repository):
+    def test_relationships(self, session, cls_, repository, tool_version_association_factory, tool_version):
+        # This test is non-standard because we must test associations that do not have relationships set up.
+        # As a result, we need the object pkey in order to setup the test, which is why we have to manually
+        # add obj to the session and flush it.
         obj = cls_()
         obj.tool_shed_repository = repository
-        # TODO
-        # parent_tool_association
-        # child_tool_association
 
-        with dbcleanup(session, obj) as obj_id:
-            stored_obj = get_stored_obj(session, cls_, obj_id)
-            assert stored_obj.tool_shed_repository.id == repository.id
+        session.add(obj)
+        session.flush()
+
+        tool_version_assoc1 = tool_version_association_factory()
+        tool_version_assoc1.tool_id = obj.id  # tool_version under test
+        tool_version_assoc1.parent_id = tool_version.id  # some other tool_version
+
+        tool_version_assoc2 = tool_version_association_factory()
+        tool_version_assoc2.tool_id = tool_version.id  # some other tool_version
+        tool_version_assoc2.parent_id = obj.id  # tool_version under test
+
+        session.add(tool_version_assoc1)
+        session.add(tool_version_assoc2)
+        session.flush()
+
+        stored_obj = get_stored_obj(session, cls_, obj.id)
+        assert stored_obj.tool_shed_repository.id == repository.id
+        assert stored_obj.parent_tool_association == [tool_version_assoc1]
+        assert stored_obj.child_tool_association == [tool_version_assoc2]
+
+        delete_from_database(session, [obj, tool_version_assoc1, tool_version_assoc2])
 
 
 class TestToolVersionAssociation(BaseTest):
@@ -326,6 +344,13 @@ def tool_version(model, session):
     yield from dbcleanup_wrapper(session, instance)
 
 
+@pytest.fixture
+def tool_version_association_factory(model):
+    def make_instance(*args, **kwds):
+        return model.ToolVersionAssociation(*args, **kwds)
+    return make_instance
+
+
 @pytest.fixture
 def tool_version_factory(model):
     def make_instance(*args, **kwds):
@@ -392,3 +417,19 @@ def _get_default_where_clause(cls, obj_id):
     # where_clause = cls.__table__.c.id == obj_id  # TODO
     where_clause = cls.table.c.id == obj_id
     return where_clause
+
+
+def delete_from_database(session, objects):
+    """
+    Delete each object in objects from database.
+    May be called at the end of a test if use of a context manager is impractical.
+    (Assume all objects have the id field as their primary key.)
+    """
+    # Ensure we have a list of objects (check for list explicitly: a model can be iterable)
+    if not isinstance(objects, list):
+        objects = [objects]
+
+    for obj in objects:
+        table = obj.__table__
+        stmt = delete(table).where(table.c.id == obj.id)
+        session.execute(stmt)

From 8f79a8fc469eb6f606bda20aa5e79a7facca9e5c Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 12:37:22 -0400
Subject: [PATCH 05/23] Remove MigrateTools from model and mapping (note)

This class is not referenced in the codebase. The table has limited use,
but not through the model, so, I think, it shouldn't be part of the
model. The table is part of our SQLAlchemy Migrate setup, which is being
replaced with Alembic.
---
 lib/galaxy/model/tool_shed_install/__init__.py | 8 --------
 lib/galaxy/model/tool_shed_install/mapping.py  | 5 -----
 2 files changed, 13 deletions(-)

diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py
index f0bc3fe373c5..cf2544129d36 100644
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -596,11 +596,3 @@ def __init__(self, id=None, tool_id=None, parent_id=None):
         self.id = id
         self.tool_id = tool_id
         self.parent_id = parent_id
-
-
-class MigrateTools(_HasTable):
-
-    def __init__(self, repository_id=None, repository_path=None, version=None):
-        self.repository_id = repository_id
-        self.repository_path = repository_path
-        self.version = version
diff --git a/lib/galaxy/model/tool_shed_install/mapping.py b/lib/galaxy/model/tool_shed_install/mapping.py
index 6b8ee051fbd0..467cf07509be 100644
--- a/lib/galaxy/model/tool_shed_install/mapping.py
+++ b/lib/galaxy/model/tool_shed_install/mapping.py
@@ -78,11 +78,6 @@
                                                    Column("tool_id", Integer, ForeignKey("tool_version.id"), index=True, nullable=False),
                                                    Column("parent_id", Integer, ForeignKey("tool_version.id"), index=True, nullable=False))
 
-install_model.MigrateTools.table = Table("migrate_tools", metadata,
-                                         Column("repository_id", TrimmedString(255)),
-                                         Column("repository_path", TEXT),
-                                         Column("version", Integer))
-
 mapper_registry.map_imperatively(install_model.ToolShedRepository, install_model.ToolShedRepository.table,
        properties=dict(tool_versions=relation(install_model.ToolVersion,
                                               primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.ToolVersion.table.c.tool_shed_repository_id),

From 86a30bc0ff451a9bba0b0ab7d9ee21e9ed7728f8 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 12:53:45 -0400
Subject: [PATCH 06/23] Map RepositoryRepositoryDependencyAssociation
 declaratively

Also, setup Base class for declarative
---
 .../model/tool_shed_install/__init__.py       | 40 ++++++++++++++++---
 lib/galaxy/model/tool_shed_install/mapping.py | 15 +------
 .../data/model/test_install_model_mapping.py  |  3 +-
 3 files changed, 37 insertions(+), 21 deletions(-)

diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py
index cf2544129d36..b85106058577 100644
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -3,8 +3,20 @@
 from enum import Enum
 from typing import TYPE_CHECKING
 
-from sqlalchemy.orm import registry
-
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    Table,
+)
+from sqlalchemy.orm import (
+    registry,
+    relationship,
+)
+from sqlalchemy.orm.decl_api import DeclarativeMeta
+
+from galaxy.model.orm.now import now
 from galaxy.util import asbool
 from galaxy.util.bunch import Bunch
 from galaxy.util.dictifiable import Dictifiable
@@ -15,14 +27,23 @@
 mapper_registry = registry()
 
 if TYPE_CHECKING:
-    from sqlalchemy.schema import Table
-
     class _HasTable:
         table: Table
 else:
     _HasTable = object
 
 
+class Base(metaclass=DeclarativeMeta):
+    __abstract__ = True
+    registry = mapper_registry
+    metadata = mapper_registry.metadata
+    __init__ = mapper_registry.constructor
+
+    @classmethod
+    def __declare_last__(cls):
+        cls.table = cls.__table__
+
+
 class ToolShedRepository(_HasTable):
     dict_collection_visible_keys = ['id', 'tool_shed', 'name', 'owner', 'installed_changeset_revision', 'changeset_revision', 'ctx_rev', 'includes_datatypes',
                                     'tool_shed_status', 'deleted', 'uninstalled', 'dist_to_shed', 'status', 'error_message', 'description']
@@ -487,7 +508,16 @@ def upgrade_available(self):
         return False
 
 
-class RepositoryRepositoryDependencyAssociation(_HasTable):
+class RepositoryRepositoryDependencyAssociation(Base, _HasTable):
+    __tablename__ = 'repository_repository_dependency_association'
+
+    id = Column(Integer, primary_key=True)
+    create_time = Column(DateTime, default=now)
+    update_time = Column(DateTime, default=now, onupdate=now)
+    tool_shed_repository_id = Column(Integer, ForeignKey('tool_shed_repository.id'), index=True)
+    repository_dependency_id = Column(Integer, ForeignKey('repository_dependency.id'), index=True)
+    repository = relationship('ToolShedRepository')
+    repository_dependency = relationship('RepositoryDependency')
 
     def __init__(self, tool_shed_repository_id=None, repository_dependency_id=None):
         self.tool_shed_repository_id = tool_shed_repository_id
diff --git a/lib/galaxy/model/tool_shed_install/mapping.py b/lib/galaxy/model/tool_shed_install/mapping.py
index 467cf07509be..c54d837bb8c7 100644
--- a/lib/galaxy/model/tool_shed_install/mapping.py
+++ b/lib/galaxy/model/tool_shed_install/mapping.py
@@ -42,13 +42,6 @@
                                                Column("status", TrimmedString(255)),
                                                Column("error_message", TEXT))
 
-install_model.RepositoryRepositoryDependencyAssociation.table = Table('repository_repository_dependency_association', metadata,
-                                                                      Column("id", Integer, primary_key=True),
-                                                                      Column("create_time", DateTime, default=now),
-                                                                      Column("update_time", DateTime, default=now, onupdate=now),
-                                                                      Column("tool_shed_repository_id", Integer, ForeignKey("tool_shed_repository.id"), index=True),
-                                                                      Column("repository_dependency_id", Integer, ForeignKey("repository_dependency.id"), index=True))
-
 install_model.RepositoryDependency.table = Table("repository_dependency", metadata,
                                                  Column("id", Integer, primary_key=True),
                                                  Column("create_time", DateTime, default=now),
@@ -87,13 +80,7 @@
                                                   order_by=install_model.ToolDependency.table.c.name,
                                                   backref='tool_shed_repository'),
                        required_repositories=relation(install_model.RepositoryRepositoryDependencyAssociation,
-                                                      primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.RepositoryRepositoryDependencyAssociation.table.c.tool_shed_repository_id))))
-
-mapper_registry.map_imperatively(install_model.RepositoryRepositoryDependencyAssociation, install_model.RepositoryRepositoryDependencyAssociation.table,
-       properties=dict(repository=relation(install_model.ToolShedRepository,
-                                           primaryjoin=(install_model.RepositoryRepositoryDependencyAssociation.table.c.tool_shed_repository_id == install_model.ToolShedRepository.table.c.id)),
-                       repository_dependency=relation(install_model.RepositoryDependency,
-                                                      primaryjoin=(install_model.RepositoryRepositoryDependencyAssociation.table.c.repository_dependency_id == install_model.RepositoryDependency.table.c.id))))
+                                                      primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.RepositoryRepositoryDependencyAssociation.tool_shed_repository_id))))
 
 mapper_registry.map_imperatively(install_model.RepositoryDependency, install_model.RepositoryDependency.table,
        properties=dict(repository=relation(install_model.ToolShedRepository,
diff --git a/test/unit/data/model/test_install_model_mapping.py b/test/unit/data/model/test_install_model_mapping.py
index 2e0898a8db70..d4b7d5c74607 100644
--- a/test/unit/data/model/test_install_model_mapping.py
+++ b/test/unit/data/model/test_install_model_mapping.py
@@ -111,8 +111,7 @@ def test_relationships(
 class TestRepositoryRepositoryDependencyAssociation(BaseTest):
 
     def test_table(self, cls_):
-        assert cls_.table.name == 'repository_repository_dependency_association'
-        # assert cls_.__tablename__ == 'repository_dependency'  # TODO
+        assert cls_.__tablename__ == 'repository_repository_dependency_association'
 
     def test_columns(self, session, cls_, repository, repository_dependency):
         create_time = datetime.now()

From a3d7a37c8e309010ddcbf70372dae27e1ff0c810 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 13:09:47 -0400
Subject: [PATCH 07/23] Map RepositoryDependency declaratively

---
 lib/galaxy/model/tool_shed_install/__init__.py     |  9 ++++++++-
 lib/galaxy/model/tool_shed_install/mapping.py      | 10 ----------
 test/unit/data/model/test_install_model_mapping.py |  3 +--
 3 files changed, 9 insertions(+), 13 deletions(-)

diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py
index b85106058577..ffd97f7fd6f9 100644
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -524,7 +524,14 @@ def __init__(self, tool_shed_repository_id=None, repository_dependency_id=None):
         self.repository_dependency_id = repository_dependency_id
 
 
-class RepositoryDependency(_HasTable):
+class RepositoryDependency(Base, _HasTable):
+    __tablename__ = 'repository_dependency'
+
+    id = Column(Integer, primary_key=True)
+    create_time = Column(DateTime, default=now)
+    update_time = Column(DateTime, default=now, onupdate=now)
+    tool_shed_repository_id = Column(Integer, ForeignKey('tool_shed_repository.id'), index=True, nullable=False)
+    repository = relationship('ToolShedRepository')
 
     def __init__(self, tool_shed_repository_id=None):
         self.tool_shed_repository_id = tool_shed_repository_id
diff --git a/lib/galaxy/model/tool_shed_install/mapping.py b/lib/galaxy/model/tool_shed_install/mapping.py
index c54d837bb8c7..60b8dba5e0dc 100644
--- a/lib/galaxy/model/tool_shed_install/mapping.py
+++ b/lib/galaxy/model/tool_shed_install/mapping.py
@@ -42,12 +42,6 @@
                                                Column("status", TrimmedString(255)),
                                                Column("error_message", TEXT))
 
-install_model.RepositoryDependency.table = Table("repository_dependency", metadata,
-                                                 Column("id", Integer, primary_key=True),
-                                                 Column("create_time", DateTime, default=now),
-                                                 Column("update_time", DateTime, default=now, onupdate=now),
-                                                 Column("tool_shed_repository_id", Integer, ForeignKey("tool_shed_repository.id"), index=True, nullable=False))
-
 install_model.ToolDependency.table = Table("tool_dependency", metadata,
                                            Column("id", Integer, primary_key=True),
                                            Column("create_time", DateTime, default=now),
@@ -82,10 +76,6 @@
                        required_repositories=relation(install_model.RepositoryRepositoryDependencyAssociation,
                                                       primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.RepositoryRepositoryDependencyAssociation.tool_shed_repository_id))))
 
-mapper_registry.map_imperatively(install_model.RepositoryDependency, install_model.RepositoryDependency.table,
-       properties=dict(repository=relation(install_model.ToolShedRepository,
-                                           primaryjoin=(install_model.RepositoryDependency.table.c.tool_shed_repository_id == install_model.ToolShedRepository.table.c.id))))
-
 mapper_registry.map_imperatively(install_model.ToolDependency, install_model.ToolDependency.table)
 
 mapper_registry.map_imperatively(install_model.ToolVersion, install_model.ToolVersion.table,
diff --git a/test/unit/data/model/test_install_model_mapping.py b/test/unit/data/model/test_install_model_mapping.py
index d4b7d5c74607..0837a79a024f 100644
--- a/test/unit/data/model/test_install_model_mapping.py
+++ b/test/unit/data/model/test_install_model_mapping.py
@@ -144,8 +144,7 @@ def test_relationships(self, session, cls_, repository, repository_dependency):
 class TestRepositoryDependency(BaseTest):
 
     def test_table(self, cls_):
-        assert cls_.table.name == 'repository_dependency'
-        # assert cls_.__tablename__ == 'repository_dependency'  # TODO
+        assert cls_.__tablename__ == 'repository_dependency'
 
     def test_columns(self, session, cls_, repository):
         create_time = datetime.now()

From 92b32bab810b62c75dbb0515e7a371f0afae7fe1 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 13:17:02 -0400
Subject: [PATCH 08/23] Map ToolDependency declaratively

---
 lib/galaxy/model/tool_shed_install/__init__.py | 18 +++++++++++++++++-
 lib/galaxy/model/tool_shed_install/mapping.py  | 17 ++---------------
 .../data/model/test_install_model_mapping.py   |  3 +--
 3 files changed, 20 insertions(+), 18 deletions(-)

diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py
index ffd97f7fd6f9..c9e427586aa5 100644
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -9,6 +9,7 @@
     ForeignKey,
     Integer,
     Table,
+    TEXT,
 )
 from sqlalchemy.orm import (
     registry,
@@ -16,6 +17,9 @@
 )
 from sqlalchemy.orm.decl_api import DeclarativeMeta
 
+from galaxy.model.custom_types import (
+    TrimmedString
+)
 from galaxy.model.orm.now import now
 from galaxy.util import asbool
 from galaxy.util.bunch import Bunch
@@ -537,7 +541,19 @@ def __init__(self, tool_shed_repository_id=None):
         self.tool_shed_repository_id = tool_shed_repository_id
 
 
-class ToolDependency(_HasTable):
+class ToolDependency(Base, _HasTable):
+    __tablename__ = 'tool_dependency'
+
+    id = Column(Integer, primary_key=True)
+    create_time = Column(DateTime, default=now)
+    update_time = Column(DateTime, default=now, onupdate=now)
+    tool_shed_repository_id = Column(Integer, ForeignKey('tool_shed_repository.id'), index=True, nullable=False)
+    name = Column(TrimmedString(255))
+    version = Column(TEXT)
+    type = Column(TrimmedString(40))
+    status = Column(TrimmedString(255), nullable=False)
+    error_message = Column(TEXT)
+
     # converting this one to Enum breaks the tool shed tests,
     # don't know why though -John
     installation_status = Bunch(NEVER_INSTALLED='Never installed',
diff --git a/lib/galaxy/model/tool_shed_install/mapping.py b/lib/galaxy/model/tool_shed_install/mapping.py
index 60b8dba5e0dc..244b3ddfb379 100644
--- a/lib/galaxy/model/tool_shed_install/mapping.py
+++ b/lib/galaxy/model/tool_shed_install/mapping.py
@@ -42,17 +42,6 @@
                                                Column("status", TrimmedString(255)),
                                                Column("error_message", TEXT))
 
-install_model.ToolDependency.table = Table("tool_dependency", metadata,
-                                           Column("id", Integer, primary_key=True),
-                                           Column("create_time", DateTime, default=now),
-                                           Column("update_time", DateTime, default=now, onupdate=now),
-                                           Column("tool_shed_repository_id", Integer, ForeignKey("tool_shed_repository.id"), index=True, nullable=False),
-                                           Column("name", TrimmedString(255)),
-                                           Column("version", TEXT),
-                                           Column("type", TrimmedString(40)),
-                                           Column("status", TrimmedString(255), nullable=False),
-                                           Column("error_message", TEXT))
-
 install_model.ToolVersion.table = Table("tool_version", metadata,
                                         Column("id", Integer, primary_key=True),
                                         Column("create_time", DateTime, default=now),
@@ -70,14 +59,12 @@
                                               primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.ToolVersion.table.c.tool_shed_repository_id),
                                               backref='tool_shed_repository'),
                        tool_dependencies=relation(install_model.ToolDependency,
-                                                  primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.ToolDependency.table.c.tool_shed_repository_id),
-                                                  order_by=install_model.ToolDependency.table.c.name,
+                                                  primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.ToolDependency.tool_shed_repository_id),
+                                                  order_by=install_model.ToolDependency.name,
                                                   backref='tool_shed_repository'),
                        required_repositories=relation(install_model.RepositoryRepositoryDependencyAssociation,
                                                       primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.RepositoryRepositoryDependencyAssociation.tool_shed_repository_id))))
 
-mapper_registry.map_imperatively(install_model.ToolDependency, install_model.ToolDependency.table)
-
 mapper_registry.map_imperatively(install_model.ToolVersion, install_model.ToolVersion.table,
        properties=dict(
            parent_tool_association=relation(install_model.ToolVersionAssociation,
diff --git a/test/unit/data/model/test_install_model_mapping.py b/test/unit/data/model/test_install_model_mapping.py
index 0837a79a024f..301869835ced 100644
--- a/test/unit/data/model/test_install_model_mapping.py
+++ b/test/unit/data/model/test_install_model_mapping.py
@@ -173,8 +173,7 @@ def test_relationships(self, session, cls_, repository):
 class TestToolDependency(BaseTest):
 
     def test_table(self, cls_):
-        assert cls_.table.name == 'tool_dependency'
-        # assert cls_.__tablename__ == 'tool_dependency'  # TODO
+        assert cls_.__tablename__ == 'tool_dependency'
 
     def test_columns(self, session, cls_, repository):
         create_time = datetime.now()

From 1fe5e6dfc8885e5638991e02dedd3cbd7eb92335 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 13:22:13 -0400
Subject: [PATCH 09/23] Map ToolVersion declaratively

---
 lib/galaxy/model/tool_shed_install/__init__.py  | 16 +++++++++++++++-
 lib/galaxy/model/tool_shed_install/mapping.py   | 17 +----------------
 .../data/model/test_install_model_mapping.py    |  3 +--
 3 files changed, 17 insertions(+), 19 deletions(-)

diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py
index c9e427586aa5..9b6177079059 100644
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -8,6 +8,7 @@
     DateTime,
     ForeignKey,
     Integer,
+    String,
     Table,
     TEXT,
 )
@@ -624,7 +625,20 @@ def is_installed(self):
         return self.status == self.installation_status.INSTALLED
 
 
-class ToolVersion(Dictifiable, _HasTable):
+class ToolVersion(Base, Dictifiable, _HasTable):
+    __tablename__ = 'tool_version'
+
+    id = Column(Integer, primary_key=True)
+    create_time = Column(DateTime, default=now)
+    update_time = Column(DateTime, default=now, onupdate=now)
+    tool_id = Column(String(255))
+    tool_shed_repository_id = Column(Integer, ForeignKey('tool_shed_repository.id'), index=True, nullable=True)
+
+    parent_tool_association = relationship('ToolVersionAssociation',
+        primaryjoin=(lambda: ToolVersion.id == ToolVersionAssociation.tool_id))  # type: ignore
+    child_tool_association = relationship('ToolVersionAssociation',
+        primaryjoin=(lambda: ToolVersion.id == ToolVersionAssociation.parent_id))  # type: ignore
+
     dict_element_visible_keys = ['id', 'tool_shed_repository']
 
     def __init__(self, id=None, create_time=None, tool_id=None, tool_shed_repository=None):
diff --git a/lib/galaxy/model/tool_shed_install/mapping.py b/lib/galaxy/model/tool_shed_install/mapping.py
index 244b3ddfb379..3f846d89bbfe 100644
--- a/lib/galaxy/model/tool_shed_install/mapping.py
+++ b/lib/galaxy/model/tool_shed_install/mapping.py
@@ -4,7 +4,6 @@
     DateTime,
     ForeignKey,
     Integer,
-    String,
     Table,
     TEXT
 )
@@ -42,13 +41,6 @@
                                                Column("status", TrimmedString(255)),
                                                Column("error_message", TEXT))
 
-install_model.ToolVersion.table = Table("tool_version", metadata,
-                                        Column("id", Integer, primary_key=True),
-                                        Column("create_time", DateTime, default=now),
-                                        Column("update_time", DateTime, default=now, onupdate=now),
-                                        Column("tool_id", String(255)),
-                                        Column("tool_shed_repository_id", Integer, ForeignKey("tool_shed_repository.id"), index=True, nullable=True))
-
 install_model.ToolVersionAssociation.table = Table("tool_version_association", metadata,
                                                    Column("id", Integer, primary_key=True),
                                                    Column("tool_id", Integer, ForeignKey("tool_version.id"), index=True, nullable=False),
@@ -56,7 +48,7 @@
 
 mapper_registry.map_imperatively(install_model.ToolShedRepository, install_model.ToolShedRepository.table,
        properties=dict(tool_versions=relation(install_model.ToolVersion,
-                                              primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.ToolVersion.table.c.tool_shed_repository_id),
+                                              primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.ToolVersion.tool_shed_repository_id),
                                               backref='tool_shed_repository'),
                        tool_dependencies=relation(install_model.ToolDependency,
                                                   primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.ToolDependency.tool_shed_repository_id),
@@ -65,13 +57,6 @@
                        required_repositories=relation(install_model.RepositoryRepositoryDependencyAssociation,
                                                       primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.RepositoryRepositoryDependencyAssociation.tool_shed_repository_id))))
 
-mapper_registry.map_imperatively(install_model.ToolVersion, install_model.ToolVersion.table,
-       properties=dict(
-           parent_tool_association=relation(install_model.ToolVersionAssociation,
-                                            primaryjoin=(install_model.ToolVersion.table.c.id == install_model.ToolVersionAssociation.table.c.tool_id)),
-           child_tool_association=relation(install_model.ToolVersionAssociation,
-                                           primaryjoin=(install_model.ToolVersion.table.c.id == install_model.ToolVersionAssociation.table.c.parent_id))))
-
 mapper_registry.map_imperatively(install_model.ToolVersionAssociation, install_model.ToolVersionAssociation.table)
 
 
diff --git a/test/unit/data/model/test_install_model_mapping.py b/test/unit/data/model/test_install_model_mapping.py
index 301869835ced..1578f6c6cdf6 100644
--- a/test/unit/data/model/test_install_model_mapping.py
+++ b/test/unit/data/model/test_install_model_mapping.py
@@ -214,8 +214,7 @@ def test_relationships(self, session, cls_, repository):
 class TestToolVersion(BaseTest):
 
     def test_table(self, cls_):
-        assert cls_.table.name == 'tool_version'
-        # assert cls_.__tablename__ == 'tool_version'  # TODO
+        assert cls_.__tablename__ == 'tool_version'
 
     def test_columns(self, session, cls_, repository):
         create_time = datetime.now()

From 191464f2fc9c38f21b6c8064206b345d8f8d863b Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 13:31:10 -0400
Subject: [PATCH 10/23] Map ToolVersionAssociation declaratively

---
 lib/galaxy/model/tool_shed_install/__init__.py     | 7 ++++++-
 lib/galaxy/model/tool_shed_install/mapping.py      | 8 --------
 test/unit/data/model/test_install_model_mapping.py | 3 +--
 3 files changed, 7 insertions(+), 11 deletions(-)

diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py
index 9b6177079059..cb569ed41714 100644
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -657,7 +657,12 @@ def to_dict(self, view='element'):
         return rval
 
 
-class ToolVersionAssociation(_HasTable):
+class ToolVersionAssociation(Base, _HasTable):
+    __tablename__ = 'tool_version_association'
+
+    id = Column(Integer, primary_key=True)
+    tool_id = Column(Integer, ForeignKey('tool_version.id'), index=True, nullable=False)
+    parent_id = Column(Integer, ForeignKey('tool_version.id'), index=True, nullable=False)
 
     def __init__(self, id=None, tool_id=None, parent_id=None):
         self.id = id
diff --git a/lib/galaxy/model/tool_shed_install/mapping.py b/lib/galaxy/model/tool_shed_install/mapping.py
index 3f846d89bbfe..9519dbc3b776 100644
--- a/lib/galaxy/model/tool_shed_install/mapping.py
+++ b/lib/galaxy/model/tool_shed_install/mapping.py
@@ -2,7 +2,6 @@
     Boolean,
     Column,
     DateTime,
-    ForeignKey,
     Integer,
     Table,
     TEXT
@@ -41,11 +40,6 @@
                                                Column("status", TrimmedString(255)),
                                                Column("error_message", TEXT))
 
-install_model.ToolVersionAssociation.table = Table("tool_version_association", metadata,
-                                                   Column("id", Integer, primary_key=True),
-                                                   Column("tool_id", Integer, ForeignKey("tool_version.id"), index=True, nullable=False),
-                                                   Column("parent_id", Integer, ForeignKey("tool_version.id"), index=True, nullable=False))
-
 mapper_registry.map_imperatively(install_model.ToolShedRepository, install_model.ToolShedRepository.table,
        properties=dict(tool_versions=relation(install_model.ToolVersion,
                                               primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.ToolVersion.tool_shed_repository_id),
@@ -57,8 +51,6 @@
                        required_repositories=relation(install_model.RepositoryRepositoryDependencyAssociation,
                                                       primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.RepositoryRepositoryDependencyAssociation.tool_shed_repository_id))))
 
-mapper_registry.map_imperatively(install_model.ToolVersionAssociation, install_model.ToolVersionAssociation.table)
-
 
 def init(url, engine_options=None, create_tables=False):
     """Connect mappings to the database"""
diff --git a/test/unit/data/model/test_install_model_mapping.py b/test/unit/data/model/test_install_model_mapping.py
index 1578f6c6cdf6..af1efdf6b975 100644
--- a/test/unit/data/model/test_install_model_mapping.py
+++ b/test/unit/data/model/test_install_model_mapping.py
@@ -267,8 +267,7 @@ def test_relationships(self, session, cls_, repository, tool_version_association
 class TestToolVersionAssociation(BaseTest):
 
     def test_table(self, cls_):
-        assert cls_.table.name == 'tool_version_association'
-        # assert cls_.__tablename__ == 'tool_version_association'  # TODO
+        assert cls_.__tablename__ == 'tool_version_association'
 
     def test_columns(self, session, cls_, tool_version_factory):
         tool_version = tool_version_factory()

From 19dc5c90927d88d6c7330ffc95a361964d6947b6 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 14:33:20 -0400
Subject: [PATCH 11/23] Remove backref from ToolShedRepository.tool_version

---
 lib/galaxy/model/tool_shed_install/__init__.py |  1 +
 lib/galaxy/model/tool_shed_install/mapping.py  | 18 ++++++++----------
 2 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py
index cb569ed41714..0a94a3e729e9 100644
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -638,6 +638,7 @@ class ToolVersion(Base, Dictifiable, _HasTable):
         primaryjoin=(lambda: ToolVersion.id == ToolVersionAssociation.tool_id))  # type: ignore
     child_tool_association = relationship('ToolVersionAssociation',
         primaryjoin=(lambda: ToolVersion.id == ToolVersionAssociation.parent_id))  # type: ignore
+    tool_shed_repository = relationship('ToolShedRepository', back_populates='tool_versions')
 
     dict_element_visible_keys = ['id', 'tool_shed_repository']
 
diff --git a/lib/galaxy/model/tool_shed_install/mapping.py b/lib/galaxy/model/tool_shed_install/mapping.py
index 9519dbc3b776..33ae1ad2f221 100644
--- a/lib/galaxy/model/tool_shed_install/mapping.py
+++ b/lib/galaxy/model/tool_shed_install/mapping.py
@@ -40,16 +40,14 @@
                                                Column("status", TrimmedString(255)),
                                                Column("error_message", TEXT))
 
-mapper_registry.map_imperatively(install_model.ToolShedRepository, install_model.ToolShedRepository.table,
-       properties=dict(tool_versions=relation(install_model.ToolVersion,
-                                              primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.ToolVersion.tool_shed_repository_id),
-                                              backref='tool_shed_repository'),
-                       tool_dependencies=relation(install_model.ToolDependency,
-                                                  primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.ToolDependency.tool_shed_repository_id),
-                                                  order_by=install_model.ToolDependency.name,
-                                                  backref='tool_shed_repository'),
-                       required_repositories=relation(install_model.RepositoryRepositoryDependencyAssociation,
-                                                      primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.RepositoryRepositoryDependencyAssociation.tool_shed_repository_id))))
+mapper_registry.map_imperatively(install_model.ToolShedRepository, install_model.ToolShedRepository.table, properties=dict(
+    tool_versions=relation(install_model.ToolVersion, back_populates='tool_shed_repository'),
+    tool_dependencies=relation(install_model.ToolDependency,
+                               primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.ToolDependency.tool_shed_repository_id),
+                               order_by=install_model.ToolDependency.name,
+                               backref='tool_shed_repository'),
+    required_repositories=relation(install_model.RepositoryRepositoryDependencyAssociation,
+                                   primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.RepositoryRepositoryDependencyAssociation.tool_shed_repository_id))))
 
 
 def init(url, engine_options=None, create_tables=False):

From f99a3972cd506fb05514d90540be09f23ea8ceda Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 14:36:22 -0400
Subject: [PATCH 12/23] Remove backref from
 ToolShedRepository.tool_dependencies

---
 lib/galaxy/model/tool_shed_install/__init__.py | 1 +
 lib/galaxy/model/tool_shed_install/mapping.py  | 6 ++----
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py
index 0a94a3e729e9..d2ce177c3b00 100644
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -554,6 +554,7 @@ class ToolDependency(Base, _HasTable):
     type = Column(TrimmedString(40))
     status = Column(TrimmedString(255), nullable=False)
     error_message = Column(TEXT)
+    tool_shed_repository = relationship('ToolShedRepository', back_populates='tool_dependencies')
 
     # converting this one to Enum breaks the tool shed tests,
     # don't know why though -John
diff --git a/lib/galaxy/model/tool_shed_install/mapping.py b/lib/galaxy/model/tool_shed_install/mapping.py
index 33ae1ad2f221..e6650d6d9c2c 100644
--- a/lib/galaxy/model/tool_shed_install/mapping.py
+++ b/lib/galaxy/model/tool_shed_install/mapping.py
@@ -42,10 +42,8 @@
 
 mapper_registry.map_imperatively(install_model.ToolShedRepository, install_model.ToolShedRepository.table, properties=dict(
     tool_versions=relation(install_model.ToolVersion, back_populates='tool_shed_repository'),
-    tool_dependencies=relation(install_model.ToolDependency,
-                               primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.ToolDependency.tool_shed_repository_id),
-                               order_by=install_model.ToolDependency.name,
-                               backref='tool_shed_repository'),
+    tool_dependencies=relation(install_model.ToolDependency, order_by=install_model.ToolDependency.name,
+        back_populates='tool_shed_repository'),
     required_repositories=relation(install_model.RepositoryRepositoryDependencyAssociation,
                                    primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.RepositoryRepositoryDependencyAssociation.tool_shed_repository_id))))
 

From cf964678b9742f2083023456ecd0efb10463633a Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 14:38:17 -0400
Subject: [PATCH 13/23] Remove unnecessary primary_join attr

---
 lib/galaxy/model/tool_shed_install/mapping.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/galaxy/model/tool_shed_install/mapping.py b/lib/galaxy/model/tool_shed_install/mapping.py
index e6650d6d9c2c..4e1f26a1a061 100644
--- a/lib/galaxy/model/tool_shed_install/mapping.py
+++ b/lib/galaxy/model/tool_shed_install/mapping.py
@@ -44,8 +44,7 @@
     tool_versions=relation(install_model.ToolVersion, back_populates='tool_shed_repository'),
     tool_dependencies=relation(install_model.ToolDependency, order_by=install_model.ToolDependency.name,
         back_populates='tool_shed_repository'),
-    required_repositories=relation(install_model.RepositoryRepositoryDependencyAssociation,
-                                   primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.RepositoryRepositoryDependencyAssociation.tool_shed_repository_id))))
+    required_repositories=relation(install_model.RepositoryRepositoryDependencyAssociation)))
 
 
 def init(url, engine_options=None, create_tables=False):

From a8e3c843f28e9ed49b239077e5250021fac81a56 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 14:43:52 -0400
Subject: [PATCH 14/23] Fix SAWarning: add back_populates args

---
 lib/galaxy/model/tool_shed_install/__init__.py | 3 +--
 lib/galaxy/model/tool_shed_install/mapping.py  | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py
index d2ce177c3b00..769b09cec7a6 100644
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -521,7 +521,7 @@ class RepositoryRepositoryDependencyAssociation(Base, _HasTable):
     update_time = Column(DateTime, default=now, onupdate=now)
     tool_shed_repository_id = Column(Integer, ForeignKey('tool_shed_repository.id'), index=True)
     repository_dependency_id = Column(Integer, ForeignKey('repository_dependency.id'), index=True)
-    repository = relationship('ToolShedRepository')
+    repository = relationship('ToolShedRepository', back_populates='required_repositories')
     repository_dependency = relationship('RepositoryDependency')
 
     def __init__(self, tool_shed_repository_id=None, repository_dependency_id=None):
@@ -634,7 +634,6 @@ class ToolVersion(Base, Dictifiable, _HasTable):
     update_time = Column(DateTime, default=now, onupdate=now)
     tool_id = Column(String(255))
     tool_shed_repository_id = Column(Integer, ForeignKey('tool_shed_repository.id'), index=True, nullable=True)
-
     parent_tool_association = relationship('ToolVersionAssociation',
         primaryjoin=(lambda: ToolVersion.id == ToolVersionAssociation.tool_id))  # type: ignore
     child_tool_association = relationship('ToolVersionAssociation',
diff --git a/lib/galaxy/model/tool_shed_install/mapping.py b/lib/galaxy/model/tool_shed_install/mapping.py
index 4e1f26a1a061..f7c1fc5d8f05 100644
--- a/lib/galaxy/model/tool_shed_install/mapping.py
+++ b/lib/galaxy/model/tool_shed_install/mapping.py
@@ -44,7 +44,7 @@
     tool_versions=relation(install_model.ToolVersion, back_populates='tool_shed_repository'),
     tool_dependencies=relation(install_model.ToolDependency, order_by=install_model.ToolDependency.name,
         back_populates='tool_shed_repository'),
-    required_repositories=relation(install_model.RepositoryRepositoryDependencyAssociation)))
+    required_repositories=relation(install_model.RepositoryRepositoryDependencyAssociation, back_populates='repository')))
 
 
 def init(url, engine_options=None, create_tables=False):

From b0446b1750cfbb87cfa99c6de798886c1a29a579 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 14:51:01 -0400
Subject: [PATCH 15/23] Drop redundant datatypes from fkeys

---
 lib/galaxy/model/tool_shed_install/__init__.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py
index 769b09cec7a6..422e03d8464c 100644
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -519,8 +519,8 @@ class RepositoryRepositoryDependencyAssociation(Base, _HasTable):
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    tool_shed_repository_id = Column(Integer, ForeignKey('tool_shed_repository.id'), index=True)
-    repository_dependency_id = Column(Integer, ForeignKey('repository_dependency.id'), index=True)
+    tool_shed_repository_id = Column(ForeignKey('tool_shed_repository.id'), index=True)
+    repository_dependency_id = Column(ForeignKey('repository_dependency.id'), index=True)
     repository = relationship('ToolShedRepository', back_populates='required_repositories')
     repository_dependency = relationship('RepositoryDependency')
 
@@ -535,7 +535,7 @@ class RepositoryDependency(Base, _HasTable):
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    tool_shed_repository_id = Column(Integer, ForeignKey('tool_shed_repository.id'), index=True, nullable=False)
+    tool_shed_repository_id = Column(ForeignKey('tool_shed_repository.id'), index=True, nullable=False)
     repository = relationship('ToolShedRepository')
 
     def __init__(self, tool_shed_repository_id=None):
@@ -548,7 +548,7 @@ class ToolDependency(Base, _HasTable):
     id = Column(Integer, primary_key=True)
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
-    tool_shed_repository_id = Column(Integer, ForeignKey('tool_shed_repository.id'), index=True, nullable=False)
+    tool_shed_repository_id = Column(ForeignKey('tool_shed_repository.id'), index=True, nullable=False)
     name = Column(TrimmedString(255))
     version = Column(TEXT)
     type = Column(TrimmedString(40))
@@ -633,7 +633,7 @@ class ToolVersion(Base, Dictifiable, _HasTable):
     create_time = Column(DateTime, default=now)
     update_time = Column(DateTime, default=now, onupdate=now)
     tool_id = Column(String(255))
-    tool_shed_repository_id = Column(Integer, ForeignKey('tool_shed_repository.id'), index=True, nullable=True)
+    tool_shed_repository_id = Column(ForeignKey('tool_shed_repository.id'), index=True, nullable=True)
     parent_tool_association = relationship('ToolVersionAssociation',
         primaryjoin=(lambda: ToolVersion.id == ToolVersionAssociation.tool_id))  # type: ignore
     child_tool_association = relationship('ToolVersionAssociation',
@@ -662,8 +662,8 @@ class ToolVersionAssociation(Base, _HasTable):
     __tablename__ = 'tool_version_association'
 
     id = Column(Integer, primary_key=True)
-    tool_id = Column(Integer, ForeignKey('tool_version.id'), index=True, nullable=False)
-    parent_id = Column(Integer, ForeignKey('tool_version.id'), index=True, nullable=False)
+    tool_id = Column(ForeignKey('tool_version.id'), index=True, nullable=False)
+    parent_id = Column(ForeignKey('tool_version.id'), index=True, nullable=False)
 
     def __init__(self, id=None, tool_id=None, parent_id=None):
         self.id = id

From 353ce421cfee69cc256fe352f26099984732debb Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 14:54:39 -0400
Subject: [PATCH 16/23] Drop redundant model constructors

---
 lib/galaxy/model/tool_shed_install/__init__.py | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py
index 422e03d8464c..d375643a6876 100644
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -642,12 +642,6 @@ class ToolVersion(Base, Dictifiable, _HasTable):
 
     dict_element_visible_keys = ['id', 'tool_shed_repository']
 
-    def __init__(self, id=None, create_time=None, tool_id=None, tool_shed_repository=None):
-        self.id = id
-        self.create_time = create_time
-        self.tool_id = tool_id
-        self.tool_shed_repository = tool_shed_repository
-
     def to_dict(self, view='element'):
         rval = super().to_dict(view=view)
         rval['tool_name'] = self.tool_id
@@ -664,8 +658,3 @@ class ToolVersionAssociation(Base, _HasTable):
     id = Column(Integer, primary_key=True)
     tool_id = Column(ForeignKey('tool_version.id'), index=True, nullable=False)
     parent_id = Column(ForeignKey('tool_version.id'), index=True, nullable=False)
-
-    def __init__(self, id=None, tool_id=None, parent_id=None):
-        self.id = id
-        self.tool_id = tool_id
-        self.parent_id = parent_id

From 3738c1a281fcbfe3aaff54a07d7bc4151652a5e1 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 15:09:23 -0400
Subject: [PATCH 17/23] Add missing delete-from-db statement

---
 test/unit/data/model/test_install_model_mapping.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/test/unit/data/model/test_install_model_mapping.py b/test/unit/data/model/test_install_model_mapping.py
index af1efdf6b975..8c5a1cc6dc25 100644
--- a/test/unit/data/model/test_install_model_mapping.py
+++ b/test/unit/data/model/test_install_model_mapping.py
@@ -288,6 +288,8 @@ def test_columns(self, session, cls_, tool_version_factory):
             assert stored_obj.tool_id == tool_version.id
             assert stored_obj.parent_id == parent_tool_version.id
 
+        delete_from_database(session, [tool_version, parent_tool_version])
+
 
 # Misc. helper fixtures.
 

From 638f9a7a1c01227db5e3507ca1321476e642af91 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 15:12:20 -0400
Subject: [PATCH 18/23] Fix import error

---
 test/unit/data/model/test_test_mapping.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/unit/data/model/test_test_mapping.py b/test/unit/data/model/test_test_mapping.py
index 5ddc28953099..e1d340b894a9 100644
--- a/test/unit/data/model/test_test_mapping.py
+++ b/test/unit/data/model/test_test_mapping.py
@@ -17,7 +17,7 @@
 from sqlalchemy.orm import registry, Session
 
 from galaxy.model import _HasTable
-from . test_mapping import (
+from . test_model_mapping import (
     are_same_entity_collections,
     dbcleanup,
     dbcleanup_wrapper,

From d870278f7c82a5138929b82f9252815a1e14647c Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 15:26:10 -0400
Subject: [PATCH 19/23] Map ToolShedRepository declaratively (see note)

Rename metadata to metadata_. This will break things.
(we are only renaming the model attribute, not the table column)
Next step: rename all instances of [ToolShedRepository].metadata in code base.
---
 .../model/tool_shed_install/__init__.py       | 60 ++++++++++++++-----
 lib/galaxy/model/tool_shed_install/mapping.py | 41 -------------
 .../data/model/test_install_model_mapping.py  |  9 ++-
 3 files changed, 48 insertions(+), 62 deletions(-)

diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py
index d375643a6876..a8c8bb46b423 100644
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -4,6 +4,7 @@
 from typing import TYPE_CHECKING
 
 from sqlalchemy import (
+    Boolean,
     Column,
     DateTime,
     ForeignKey,
@@ -19,6 +20,7 @@
 from sqlalchemy.orm.decl_api import DeclarativeMeta
 
 from galaxy.model.custom_types import (
+    MutableJSONType,
     TrimmedString
 )
 from galaxy.model.orm.now import now
@@ -49,7 +51,33 @@ def __declare_last__(cls):
         cls.table = cls.__table__
 
 
-class ToolShedRepository(_HasTable):
+class ToolShedRepository(Base, _HasTable):
+    __tablename__ = 'tool_shed_repository'
+
+    id = Column(Integer, primary_key=True)
+    create_time = Column(DateTime, default=now)
+    update_time = Column(DateTime, default=now, onupdate=now)
+    tool_shed = Column(TrimmedString(255), index=True)
+    name = Column(TrimmedString(255), index=True)
+    description = Column(TEXT)
+    owner = Column(TrimmedString(255), index=True)
+    installed_changeset_revision = Column(TrimmedString(255))
+    changeset_revision = Column(TrimmedString(255), index=True)
+    ctx_rev = Column(TrimmedString(10))
+    metadata_ = Column('metadata', MutableJSONType, nullable=True)
+    includes_datatypes = Column(Boolean, index=True, default=False)
+    tool_shed_status = Column(MutableJSONType, nullable=True)
+    deleted = Column(Boolean, index=True, default=False)
+    uninstalled = Column(Boolean, default=False)
+    dist_to_shed = Column(Boolean, default=False)
+    status = Column(TrimmedString(255))
+    error_message = Column(TEXT)
+    tool_versions = relationship('ToolVersion', back_populates='tool_shed_repository')
+    tool_dependencies = relationship('ToolDependency', order_by='ToolDependency.name',
+        back_populates='tool_shed_repository')
+    required_repositories = relationship('RepositoryRepositoryDependencyAssociation',
+        back_populates='repository')
+
     dict_collection_visible_keys = ['id', 'tool_shed', 'name', 'owner', 'installed_changeset_revision', 'changeset_revision', 'ctx_rev', 'includes_datatypes',
                                     'tool_shed_status', 'deleted', 'uninstalled', 'dist_to_shed', 'status', 'error_message', 'description']
     dict_element_visible_keys = ['id', 'tool_shed', 'name', 'owner', 'installed_changeset_revision', 'changeset_revision', 'ctx_rev', 'includes_datatypes',
@@ -75,7 +103,7 @@ class states(str, Enum):
         UNINSTALLED = 'deleted_new'
 
     def __init__(self, id=None, create_time=None, tool_shed=None, name=None, description=None, owner=None, installed_changeset_revision=None,
-                 changeset_revision=None, ctx_rev=None, metadata=None, includes_datatypes=False, tool_shed_status=None, deleted=False,
+                 changeset_revision=None, ctx_rev=None, metadata_=None, includes_datatypes=False, tool_shed_status=None, deleted=False,
                  uninstalled=False, dist_to_shed=False, status=None, error_message=None):
         self.id = id
         self.create_time = create_time
@@ -86,7 +114,7 @@ def __init__(self, id=None, create_time=None, tool_shed=None, name=None, descrip
         self.installed_changeset_revision = installed_changeset_revision
         self.changeset_revision = changeset_revision
         self.ctx_rev = ctx_rev
-        self.metadata = metadata or {}
+        self.metadata_ = metadata_ or {}
         self.includes_datatypes = includes_datatypes
         self.tool_shed_status = tool_shed_status
         self.deleted = deleted
@@ -125,11 +153,11 @@ def get_sharable_url(self, app):
 
     @property
     def shed_config_filename(self):
-        return self.metadata.get('shed_config_filename')
+        return self.metadata_.get('shed_config_filename')
 
     @shed_config_filename.setter
     def shed_config_filename(self, value):
-        self.metadata['shed_config_filename'] = os.path.abspath(value)
+        self.metadata_['shed_config_filename'] = os.path.abspath(value)
 
     def get_shed_config_dict(self, app):
         """
@@ -154,7 +182,7 @@ def get_tool_relative_path(self, app):
 
     def guess_shed_config(self, app):
         tool_ids = []
-        for tool in self.metadata.get('tools', []):
+        for tool in self.metadata_.get('tools', []):
             tool_ids.append(tool.get('guid'))
         for shed_tool_conf_dict in app.toolbox.dynamic_confs(include_migrated_tool_conf=True):
             name = shed_tool_conf_dict['config_filename']
@@ -187,11 +215,11 @@ def guess_shed_config(self, app):
 
     @property
     def has_readme_files(self):
-        return 'readme_files' in self.metadata
+        return 'readme_files' in self.metadata_
 
     @property
     def has_repository_dependencies(self):
-        repository_dependencies_dict = self.metadata.get('repository_dependencies', {})
+        repository_dependencies_dict = self.metadata_.get('repository_dependencies', {})
         repository_dependencies = repository_dependencies_dict.get('repository_dependencies', [])
         # [["http://localhost:9009", "package_libgtextutils_0_6", "test", "e2003cbf18cd", "True", "True"]]
         for rd_tup in repository_dependencies:
@@ -203,7 +231,7 @@ def has_repository_dependencies(self):
 
     @property
     def has_repository_dependencies_only_if_compiling_contained_td(self):
-        repository_dependencies_dict = self.metadata.get('repository_dependencies', {})
+        repository_dependencies_dict = self.metadata_.get('repository_dependencies', {})
         repository_dependencies = repository_dependencies_dict.get('repository_dependencies', [])
         # [["http://localhost:9009", "package_libgtextutils_0_6", "test", "e2003cbf18cd", "True", "True"]]
         for rd_tup in repository_dependencies:
@@ -219,16 +247,16 @@ def in_error_state(self):
 
     @property
     def includes_data_managers(self):
-        return bool(len(self.metadata.get('data_manager', {}).get('data_managers', {})))
+        return bool(len(self.metadata_.get('data_manager', {}).get('data_managers', {})))
 
     @property
     def includes_tools(self):
-        return 'tools' in self.metadata
+        return 'tools' in self.metadata_
 
     @property
     def includes_tools_for_display_in_tool_panel(self):
         if self.includes_tools:
-            tool_dicts = self.metadata['tools']
+            tool_dicts = self.metadata_['tools']
             for tool_dict in tool_dicts:
                 if tool_dict.get('add_to_tool_panel', True):
                     return True
@@ -236,11 +264,11 @@ def includes_tools_for_display_in_tool_panel(self):
 
     @property
     def includes_tool_dependencies(self):
-        return 'tool_dependencies' in self.metadata
+        return 'tool_dependencies' in self.metadata_
 
     @property
     def includes_workflows(self):
-        return 'workflows' in self.metadata
+        return 'workflows' in self.metadata_
 
     @property
     def installed_repository_dependencies(self):
@@ -379,7 +407,7 @@ def requires_prior_installation_of(self):
         """
         required_rd_tups_that_must_be_installed = []
         if self.has_repository_dependencies:
-            rd_tups = self.metadata['repository_dependencies']['repository_dependencies']
+            rd_tups = self.metadata_['repository_dependencies']['repository_dependencies']
             for rd_tup in rd_tups:
                 if len(rd_tup) == 5:
                     tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
@@ -476,7 +504,7 @@ def tuples_of_repository_dependencies_needed_for_compiling_td(self):
         dependencies.
         """
         rd_tups_of_repositories_needed_for_compiling_td = []
-        repository_dependencies = self.metadata.get('repository_dependencies', {})
+        repository_dependencies = self.metadata_.get('repository_dependencies', {})
         rd_tups = repository_dependencies.get('repository_dependencies', [])
         for rd_tup in rd_tups:
             if len(rd_tup) == 6:
diff --git a/lib/galaxy/model/tool_shed_install/mapping.py b/lib/galaxy/model/tool_shed_install/mapping.py
index f7c1fc5d8f05..4ed7f2c9d040 100644
--- a/lib/galaxy/model/tool_shed_install/mapping.py
+++ b/lib/galaxy/model/tool_shed_install/mapping.py
@@ -1,51 +1,10 @@
-from sqlalchemy import (
-    Boolean,
-    Column,
-    DateTime,
-    Integer,
-    Table,
-    TEXT
-)
-from sqlalchemy.orm import relation
-
 from galaxy.model import tool_shed_install as install_model
 from galaxy.model.base import ModelMapping
-from galaxy.model.custom_types import (
-    MutableJSONType,
-    TrimmedString
-)
 from galaxy.model.orm.engine_factory import build_engine
-from galaxy.model.orm.now import now
 from galaxy.model.tool_shed_install import mapper_registry
 
 metadata = mapper_registry.metadata
 
-install_model.ToolShedRepository.table = Table("tool_shed_repository", metadata,
-                                               Column("id", Integer, primary_key=True),
-                                               Column("create_time", DateTime, default=now),
-                                               Column("update_time", DateTime, default=now, onupdate=now),
-                                               Column("tool_shed", TrimmedString(255), index=True),
-                                               Column("name", TrimmedString(255), index=True),
-                                               Column("description", TEXT),
-                                               Column("owner", TrimmedString(255), index=True),
-                                               Column("installed_changeset_revision", TrimmedString(255)),
-                                               Column("changeset_revision", TrimmedString(255), index=True),
-                                               Column("ctx_rev", TrimmedString(10)),
-                                               Column("metadata", MutableJSONType, nullable=True),
-                                               Column("includes_datatypes", Boolean, index=True, default=False),
-                                               Column("tool_shed_status", MutableJSONType, nullable=True),
-                                               Column("deleted", Boolean, index=True, default=False),
-                                               Column("uninstalled", Boolean, default=False),
-                                               Column("dist_to_shed", Boolean, default=False),
-                                               Column("status", TrimmedString(255)),
-                                               Column("error_message", TEXT))
-
-mapper_registry.map_imperatively(install_model.ToolShedRepository, install_model.ToolShedRepository.table, properties=dict(
-    tool_versions=relation(install_model.ToolVersion, back_populates='tool_shed_repository'),
-    tool_dependencies=relation(install_model.ToolDependency, order_by=install_model.ToolDependency.name,
-        back_populates='tool_shed_repository'),
-    required_repositories=relation(install_model.RepositoryRepositoryDependencyAssociation, back_populates='repository')))
-
 
 def init(url, engine_options=None, create_tables=False):
     """Connect mappings to the database"""
diff --git a/test/unit/data/model/test_install_model_mapping.py b/test/unit/data/model/test_install_model_mapping.py
index 8c5a1cc6dc25..7e6b10436b36 100644
--- a/test/unit/data/model/test_install_model_mapping.py
+++ b/test/unit/data/model/test_install_model_mapping.py
@@ -26,8 +26,7 @@ def cls_(self, model):
 class TestToolShedRepository(BaseTest):
 
     def test_table(self, cls_):
-        assert cls_.table.name == 'tool_shed_repository'
-        # assert cls_.__tablename__ == 'tool_shed_repository'  # TODO
+        assert cls_.__tablename__ == 'tool_shed_repository'
 
     def test_columns(self, session, cls_, repository):
         create_time = datetime.now()
@@ -39,7 +38,7 @@ def test_columns(self, session, cls_, repository):
         installed_changeset_revision = 'e'
         changeset_revision = 'f'
         ctx_rev = 'g'
-        metadata = 'h'
+        metadata_ = 'h'
         includes_datatypes = True
         tool_shed_status = 'i'
         deleted = True
@@ -58,7 +57,7 @@ def test_columns(self, session, cls_, repository):
         obj.installed_changeset_revision = installed_changeset_revision
         obj.changeset_revision = changeset_revision
         obj.ctx_rev = ctx_rev
-        obj.metadata = metadata
+        obj.metadata_ = metadata_
         obj.includes_datatypes = includes_datatypes
         obj.tool_shed_status = tool_shed_status
         obj.deleted = deleted
@@ -79,7 +78,7 @@ def test_columns(self, session, cls_, repository):
             assert stored_obj.installed_changeset_revision == installed_changeset_revision
             assert stored_obj.changeset_revision == changeset_revision
             assert stored_obj.ctx_rev == ctx_rev
-            assert stored_obj.metadata == metadata
+            assert stored_obj.metadata_ == metadata_
             assert stored_obj.includes_datatypes == includes_datatypes
             assert stored_obj.tool_shed_status == tool_shed_status
             assert stored_obj.deleted == deleted

From 691a3f6599ee91d3e751031366506e87cae182f2 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 16:44:20 -0400
Subject: [PATCH 20/23] Remove refs to ToolShedRepository.metadata in test/

---
 test/unit/app/tools/conftest.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/unit/app/tools/conftest.py b/test/unit/app/tools/conftest.py
index 3fa0f7060480..9d645a728eca 100644
--- a/test/unit/app/tools/conftest.py
+++ b/test/unit/app/tools/conftest.py
@@ -56,7 +56,7 @@ def create_repo(session, changeset, installed_changeset, config_filename=None):
     }
     if config_filename:
         metadata['shed_config_filename'] = config_filename
-    repository = tool_shed_install.ToolShedRepository(metadata=metadata)
+    repository = tool_shed_install.ToolShedRepository(metadata_=metadata)
     repository.tool_shed = "github.com"
     repository.owner = "galaxyproject"
     repository.name = "example"

From 5acbb140b16485f1f46a39df80f07af8a3e7839d Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 16:45:53 -0400
Subject: [PATCH 21/23] Remove refs to ToolShedRepository.metadata in scripts/

---
 scripts/update_shed_config_path.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/update_shed_config_path.py b/scripts/update_shed_config_path.py
index cfe4143df723..e7626b8450e9 100644
--- a/scripts/update_shed_config_path.py
+++ b/scripts/update_shed_config_path.py
@@ -16,9 +16,9 @@ def main(opts, session, model):
     Find all tool shed repositories with the bad path and update with the correct path.
     '''
     for row in session.query(model.ToolShedRepository).all():
-        if 'shed_config_filename' in row.metadata:
-            if row.metadata['shed_config_filename'] == opts.bad_filename:
-                row.metadata['shed_config_filename'] = opts.good_filename
+        if 'shed_config_filename' in row.metadata_:
+            if row.metadata_['shed_config_filename'] == opts.bad_filename:
+                row.metadata_['shed_config_filename'] = opts.good_filename
                 session.add(row)
                 session.flush()
     return 0

From bd765b0b24c8285b500cbf95a5eedaaacbeb3a4a Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 18:51:46 -0400
Subject: [PATCH 22/23] Replace all remaining instances of TSR.metadata

---
 .../datatypes/custom_datatype_manager.py               |  2 +-
 lib/galaxy/tool_shed/galaxy_install/install_manager.py |  6 +++---
 .../galaxy_install/installed_repository_manager.py     | 10 +++++-----
 .../metadata/installed_repository_metadata_manager.py  |  4 ++--
 .../repository_dependency_manager.py                   |  4 ++--
 .../tool_shed/galaxy_install/tool_migration_manager.py |  2 +-
 .../tool_shed/galaxy_install/tools/data_manager.py     |  2 +-
 .../galaxy_install/tools/tool_panel_manager.py         |  6 +++---
 .../galaxy_install/update_repository_manager.py        |  2 +-
 lib/galaxy/tool_shed/metadata/metadata_generator.py    |  2 +-
 lib/galaxy/tool_shed/util/repository_util.py           |  4 ++--
 lib/galaxy/tools/cache.py                              |  2 +-
 .../webapps/galaxy/controllers/admin_toolshed.py       |  6 +++---
 test/unit/app/tools/test_toolbox.py                    |  2 +-
 14 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/lib/galaxy/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py b/lib/galaxy/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
index 35f037e99446..a1350c3dedf6 100644
--- a/lib/galaxy/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
@@ -154,7 +154,7 @@ def load_installed_datatypes(self, repository, relative_install_dir, deactivate=
         Load proprietary datatypes and return information needed for loading custom
         datatypes converters and display applications later.
         """
-        metadata = repository.metadata
+        metadata = repository.metadata_
         repository_dict = None
         datatypes_config = get_config_from_disk(DATATYPES_CONFIG_FILENAME, relative_install_dir)
         if datatypes_config:
diff --git a/lib/galaxy/tool_shed/galaxy_install/install_manager.py b/lib/galaxy/tool_shed/galaxy_install/install_manager.py
index 73bf0067af87..66388d53f681 100644
--- a/lib/galaxy/tool_shed/galaxy_install/install_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/install_manager.py
@@ -515,7 +515,7 @@ def __handle_repository_contents(self, tool_shed_repository, tool_path, reposito
                                                   persist=True)
         irmm.generate_metadata_for_changeset_revision()
         irmm_metadata_dict = irmm.get_metadata_dict()
-        tool_shed_repository.metadata = irmm_metadata_dict
+        tool_shed_repository.metadata_ = irmm_metadata_dict
         # Update the tool_shed_repository.tool_shed_status column in the database.
         tool_shed_status_dict = repository_util.get_tool_shed_status_for_installed_repository(self.app, tool_shed_repository)
         if tool_shed_status_dict:
@@ -934,7 +934,7 @@ def install_tool_shed_repository(self, tool_shed_repository, repo_info_dict, too
                                           shed_tool_conf=shed_tool_conf,
                                           reinstalling=reinstalling,
                                           tool_panel_section_mapping=tool_panel_section_mapping)
-        metadata = tool_shed_repository.metadata
+        metadata = tool_shed_repository.metadata_
         if 'tools' in metadata and install_resolver_dependencies:
             self.update_tool_shed_repository_status(tool_shed_repository,
                                                     self.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES)
@@ -964,7 +964,7 @@ def install_tool_shed_repository(self, tool_shed_repository, repo_info_dict, too
     def update_tool_shed_repository(self, repository, tool_shed_url, latest_ctx_rev, latest_changeset_revision,
                                     install_new_dependencies=True, install_options=None):
         install_options = install_options or {}
-        original_metadata_dict = repository.metadata
+        original_metadata_dict = repository.metadata_
         original_repository_dependencies_dict = original_metadata_dict.get('repository_dependencies', {})
         original_repository_dependencies = original_repository_dependencies_dict.get('repository_dependencies', [])
         original_tool_dependencies_dict = original_metadata_dict.get('tool_dependencies', {})
diff --git a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
index 26b379d2573e..d3e594d325e0 100644
--- a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
@@ -87,10 +87,10 @@ def activate_repository(self, repository):
                                                       tpm=tpm,
                                                       repository=repository,
                                                       changeset_revision=repository.changeset_revision,
-                                                      metadata_dict=repository.metadata)
+                                                      metadata_dict=repository.metadata_)
             repository_tools_tups = irmm.get_repository_tools_tups()
             # Reload tools into the appropriate tool panel section.
-            tool_panel_dict = repository.metadata['tool_panel_section']
+            tool_panel_dict = repository.metadata_['tool_panel_section']
             tpm.add_to_tool_panel(repository.name,
                                   repository_clone_url,
                                   repository.installed_changeset_revision,
@@ -105,7 +105,7 @@ def activate_repository(self, repository):
                 data_manager_relative_install_dir = os.path.join(data_manager_relative_install_dir, repository.name)
                 dmh = data_manager.DataManagerHandler(self.app)
                 dmh.install_data_managers(self.app.config.shed_data_manager_config_file,
-                                          repository.metadata,
+                                          repository.metadata_,
                                           repository.get_shed_config_dict(self.app),
                                           data_manager_relative_install_dir,
                                           repository,
@@ -204,7 +204,7 @@ def get_dependencies_for_repository(self, tool_shed_url, repo_info_dict, include
                                                                                         name,
                                                                                         repository_owner,
                                                                                         changeset_revision)
-            if not updating and repository and repository.metadata:
+            if not updating and repository and repository.metadata_:
                 installed_rd, missing_rd = self.get_installed_and_missing_repository_dependencies(repository)
             else:
                 installed_rd, missing_rd = \
@@ -286,7 +286,7 @@ def get_installed_and_missing_repository_dependencies(self, repository):
         if has_repository_dependencies:
             # The repository dependencies container will include only the immediate repository
             # dependencies of this repository, so the container will be only a single level in depth.
-            metadata = repository.metadata
+            metadata = repository.metadata_
             installed_rd_tups = []
             missing_rd_tups = []
             for tsr in repository.repository_dependencies:
diff --git a/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py b/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
index 6619ef987734..b1a33244e91d 100644
--- a/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
@@ -87,10 +87,10 @@ def get_repository_tools_tups(self):
     def reset_all_metadata_on_installed_repository(self):
         """Reset all metadata on a single tool shed repository installed into a Galaxy instance."""
         if self.relative_install_dir:
-            original_metadata_dict = self.repository.metadata
+            original_metadata_dict = self.repository.metadata_
             self.generate_metadata_for_changeset_revision()
             if self.metadata_dict != original_metadata_dict:
-                self.repository.metadata = self.metadata_dict
+                self.repository.metadata_ = self.metadata_dict
                 self.update_in_shed_tool_config()
                 self.app.install_model.context.add(self.repository)
                 self.app.install_model.context.flush()
diff --git a/lib/galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py b/lib/galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
index 97dd25cd1e58..3e552c203a38 100644
--- a/lib/galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
@@ -233,10 +233,10 @@ def create_repository_dependency_objects(self, tool_path, tool_shed_url, repo_in
                         # The database record for the tool shed repository currently being processed can be updated.
                         # Get the repository metadata to see where it was previously located in the tool panel.
                         tpm = tool_panel_manager.ToolPanelManager(self.app)
-                        if repository_db_record and repository_db_record.metadata:
+                        if repository_db_record and repository_db_record.metadata_:
                             _, tool_panel_section_key = \
                                 tpm.handle_tool_panel_selection(toolbox=self.app.toolbox,
-                                                                metadata=repository_db_record.metadata,
+                                                                metadata=repository_db_record.metadata_,
                                                                 no_changes_checked=no_changes_checked,
                                                                 tool_panel_section_id=tool_panel_section_id,
                                                                 new_tool_panel_section_label=new_tool_panel_section_label)
diff --git a/lib/galaxy/tool_shed/galaxy_install/tool_migration_manager.py b/lib/galaxy/tool_shed/galaxy_install/tool_migration_manager.py
index f7e49548d507..f0ed910e5095 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tool_migration_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tool_migration_manager.py
@@ -442,7 +442,7 @@ def handle_repository_contents(self, tool_shed_repository, repository_clone_url,
                                                   persist=True)
         irmm.generate_metadata_for_changeset_revision()
         irmm_metadata_dict = irmm.get_metadata_dict()
-        tool_shed_repository.metadata = irmm_metadata_dict
+        tool_shed_repository.metadata_ = irmm_metadata_dict
         self.app.install_model.context.add(tool_shed_repository)
         self.app.install_model.context.flush()
         has_tool_dependencies = self.__has_tool_dependencies(irmm_metadata_dict)
diff --git a/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py b/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py
index 343b2fb081db..eff5a432122a 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py
@@ -149,7 +149,7 @@ def install_data_managers(self, shed_data_manager_conf_filename, metadata_dict,
         return rval
 
     def remove_from_data_manager(self, repository):
-        metadata_dict = repository.metadata
+        metadata_dict = repository.metadata_
         if metadata_dict and 'data_manager' in metadata_dict:
             shed_data_manager_conf_filename = self.app.config.shed_data_manager_config_file
             tree, error_message = parse_xml(shed_data_manager_conf_filename)
diff --git a/lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py b/lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py
index ba50383aa64e..e97052a17096 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py
@@ -212,7 +212,7 @@ def generate_tool_panel_dict_from_shed_tool_conf_entries(self, repository):
         tool_panel_dict = {}
         shed_tool_conf, tool_path, relative_install_dir = \
             get_tool_panel_config_tool_path_install_dir(self.app, repository)
-        metadata = repository.metadata
+        metadata = repository.metadata_
         # Create a dictionary of tool guid and tool config file name for each tool in the repository.
         guids_and_configs = {}
         if 'tools' in metadata:
@@ -467,7 +467,7 @@ def remove_repository_contents(self, repository, shed_tool_conf, uninstall):
         # information so the tools can be displayed in the same way when the repository is
         # activated or reinstalled.
         tool_panel_dict = self.generate_tool_panel_dict_from_shed_tool_conf_entries(repository)
-        repository.metadata['tool_panel_section'] = tool_panel_dict
+        repository.metadata_['tool_panel_section'] = tool_panel_dict
         self.app.install_model.context.add(repository)
         self.app.install_model.context.flush()
         # Create a list of guids for all tools that will be removed from the in-memory tool panel
@@ -481,7 +481,7 @@ def remove_repository_contents(self, repository, shed_tool_conf, uninstall):
         shed_tool_conf_dict = self.get_shed_tool_conf_dict(shed_tool_conf)
         if uninstall:
             # Remove from the shed_tool_conf file on disk.
-            self.remove_from_shed_tool_config(shed_tool_conf_dict, repository.metadata)
+            self.remove_from_shed_tool_config(shed_tool_conf_dict, repository.metadata_)
 
     def update_tool_panel_dict(self, tool_panel_dict, tool_panel_section_mapping, repository_tools_tups):
         for tool_guid in tool_panel_dict:
diff --git a/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py b/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py
index d780853de85f..392628b51d26 100644
--- a/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py
@@ -109,7 +109,7 @@ def update_repository_record(self, repository, updated_metadata_dict, updated_ch
         Update a tool_shed_repository database record with new information retrieved from the
         Tool Shed.  This happens when updating an installed repository to a new changeset revision.
         """
-        repository.metadata = updated_metadata_dict
+        repository.metadata_ = updated_metadata_dict
         tool_shed_url = get_tool_shed_url_from_tool_shed_registry(self.app, repository.tool_shed)
         clean_dependency_relationships(self.app, updated_metadata_dict, repository, tool_shed_url)
         # Update the repository.changeset_revision column in the database.
diff --git a/lib/galaxy/tool_shed/metadata/metadata_generator.py b/lib/galaxy/tool_shed/metadata/metadata_generator.py
index 98e18c109718..906799c2ce0c 100644
--- a/lib/galaxy/tool_shed/metadata/metadata_generator.py
+++ b/lib/galaxy/tool_shed/metadata/metadata_generator.py
@@ -317,7 +317,7 @@ def generate_metadata_for_changeset_revision(self):
         if self.updating_installed_repository:
             # Keep the original tool shed repository metadata if setting metadata on a repository
             # installed into a local Galaxy instance for which we have pulled updates.
-            original_repository_metadata = self.repository.metadata
+            original_repository_metadata = self.repository.metadata_
         else:
             original_repository_metadata = None
         readme_file_names = _get_readme_file_names(str(self.repository.name))
diff --git a/lib/galaxy/tool_shed/util/repository_util.py b/lib/galaxy/tool_shed/util/repository_util.py
index dcad79e1ce00..a32b8f227c78 100644
--- a/lib/galaxy/tool_shed/util/repository_util.py
+++ b/lib/galaxy/tool_shed/util/repository_util.py
@@ -112,7 +112,7 @@ def create_or_update_tool_shed_repository(app, name, description, installed_chan
         tool_shed_repository.description = description
         tool_shed_repository.changeset_revision = current_changeset_revision
         tool_shed_repository.ctx_rev = ctx_rev
-        tool_shed_repository.metadata = metadata_dict
+        tool_shed_repository.metadata_ = metadata_dict
         tool_shed_repository.includes_datatypes = includes_datatypes
         tool_shed_repository.deleted = deleted
         tool_shed_repository.uninstalled = uninstalled
@@ -127,7 +127,7 @@ def create_or_update_tool_shed_repository(app, name, description, installed_chan
                                                  installed_changeset_revision=installed_changeset_revision,
                                                  changeset_revision=current_changeset_revision,
                                                  ctx_rev=ctx_rev,
-                                                 metadata=metadata_dict,
+                                                 metadata_=metadata_dict,
                                                  includes_datatypes=includes_datatypes,
                                                  dist_to_shed=dist_to_shed,
                                                  deleted=deleted,
diff --git a/lib/galaxy/tools/cache.py b/lib/galaxy/tools/cache.py
index 25a551d7f4bd..199e5e2688a3 100644
--- a/lib/galaxy/tools/cache.py
+++ b/lib/galaxy/tools/cache.py
@@ -301,7 +301,7 @@ def add_local_repository(self, repository):
 
     def rebuild(self):
         self.repositories = self.session.query(ToolShedRepository).options(
-            defer(ToolShedRepository.metadata), joinedload('tool_dependencies')
+            defer(ToolShedRepository.metadata_), joinedload('tool_dependencies')
         ).all()
         repos_by_tuple = defaultdict(list)
         for repository in self.repositories + self.local_repositories:
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index 7e92798353cd..de0d6831c5d0 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -177,7 +177,7 @@ def view_tool_metadata(self, trans, repository_id, tool_id, **kwd):
         message = escape(kwd.get('message', ''))
         status = kwd.get('status', 'done')
         repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
-        repository_metadata = repository.metadata
+        repository_metadata = repository.metadata_
         shed_config_dict = repository.get_shed_config_dict(trans.app)
         tool_metadata = {}
         tool_lineage = []
@@ -863,7 +863,7 @@ def reinstall_repository(self, trans, **kwd):
         new_tool_panel_section_label = kwd.get('new_tool_panel_section_label', '')
         tool_panel_section_key = None
         tool_panel_section_keys = []
-        metadata = tool_shed_repository.metadata
+        metadata = tool_shed_repository.metadata_
         # Keep track of tool dependencies defined for the current repository or those defined for any of
         # its repository dependencies.
         includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies
@@ -1024,7 +1024,7 @@ def reselect_tool_panel_section(self, trans, **kwd):
         latest_ctx_rev = kwd.get('latest_ctx_rev', None)
         tool_shed_repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
         repository_clone_url = common_util.generate_clone_url_for_installed_repository(trans.app, tool_shed_repository)
-        metadata = tool_shed_repository.metadata
+        metadata = tool_shed_repository.metadata_
         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, str(tool_shed_repository.tool_shed))
         tool_path = tool_shed_repository.get_tool_relative_path(trans.app)[0]
         if latest_changeset_revision and latest_ctx_rev:
diff --git a/test/unit/app/tools/test_toolbox.py b/test/unit/app/tools/test_toolbox.py
index e99349b2504a..f1d767a44908 100644
--- a/test/unit/app/tools/test_toolbox.py
+++ b/test/unit/app/tools/test_toolbox.py
@@ -111,7 +111,7 @@ def _repo_install(self, changeset, config_filename=None):
         }
         if config_filename:
             metadata['shed_config_filename'] = config_filename
-        repository = tool_shed_install.ToolShedRepository(metadata=metadata)
+        repository = tool_shed_install.ToolShedRepository(metadata_=metadata)
         repository.tool_shed = DEFAULT_TEST_REPO.tool_shed
         repository.owner = DEFAULT_TEST_REPO.owner
         repository.name = DEFAULT_TEST_REPO.name

From 404bac39037e875af488004efa92739490f6509a Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 20 Oct 2021 20:25:28 -0400
Subject: [PATCH 23/23] Fix .metadata_ in tool_shed dir

---
 lib/tool_shed/galaxy_install/dependency_display.py   |  4 ++--
 lib/tool_shed/test/base/twilltestcase.py             | 12 ++++++------
 .../test/functional/test_1070_invalid_tool.py        |  2 +-
 .../test/functional/test_1300_reset_all_metadata.py  |  8 ++++----
 lib/tool_shed/util/shed_util_common.py               |  2 +-
 5 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/lib/tool_shed/galaxy_install/dependency_display.py b/lib/tool_shed/galaxy_install/dependency_display.py
index b7b610cb6de1..e88f789a9309 100644
--- a/lib/tool_shed/galaxy_install/dependency_display.py
+++ b/lib/tool_shed/galaxy_install/dependency_display.py
@@ -441,7 +441,7 @@ def populate_containers_dict_from_repository_metadata(self, tool_shed_url, tool_
         when displaying repository dependencies for installed repositories and when displaying
         them for uninstalled repositories that are being reinstalled.
         """
-        metadata = repository.metadata
+        metadata = repository.metadata_
         if metadata:
             # Handle proprietary datatypes.
             datatypes = metadata.get('datatypes', None)
@@ -464,7 +464,7 @@ def populate_containers_dict_from_repository_metadata(self, tool_shed_url, tool_
                     readme_files_dict = readme_util.build_readme_files_dict(self.app,
                                                                             repository,
                                                                             repository.changeset_revision,
-                                                                            repository.metadata, tool_path)
+                                                                            repository.metadata_, tool_path)
             else:
                 readme_files_dict = None
             # Handle repository dependencies.
diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 2f091fd62417..c8e505501089 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -321,7 +321,7 @@ def check_galaxy_repository_db_status(self, repository_name, owner, expected_sta
             (installed_repository.status, expected_status)
 
     def check_galaxy_repository_tool_panel_section(self, repository, expected_tool_panel_section):
-        metadata = repository.metadata
+        metadata = repository.metadata_
         assert 'tools' in metadata, f'Tools not found in repository metadata: {metadata}'
         # If integrated_tool_panel.xml is to be tested, this test method will need to be enhanced to handle tools
         # from the same repository in different tool panel sections. Getting the first tool guid is ok, because
@@ -571,7 +571,7 @@ def display_galaxy_browse_repositories_page(self, strings_displayed=None, string
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def display_installed_jobs_list_page(self, installed_repository, data_manager_names=None, strings_displayed=None, strings_not_displayed=None):
-        data_managers = installed_repository.metadata.get('data_manager', {}).get('data_managers', {})
+        data_managers = installed_repository.metadata_.get('data_manager', {}).get('data_managers', {})
         if data_manager_names:
             if not isinstance(data_manager_names, list):
                 data_manager_names = [data_manager_names]
@@ -1500,14 +1500,14 @@ def verify_installed_repositories(self, installed_repositories=None, uninstalled
 
     def verify_installed_repository_metadata_unchanged(self, name, owner):
         installed_repository = test_db_util.get_installed_repository_by_name_owner(name, owner)
-        metadata = installed_repository.metadata
+        metadata = installed_repository.metadata_
         self.reset_installed_repository_metadata(installed_repository)
-        new_metadata = installed_repository.metadata
+        new_metadata = installed_repository.metadata_
         assert metadata == new_metadata, f'Metadata for installed repository {name} differs after metadata reset.'
 
     def verify_installed_repository_no_tool_panel_section(self, repository):
         '''Verify that there is no 'tool_panel_section' entry in the repository metadata.'''
-        metadata = repository.metadata
+        metadata = repository.metadata_
         assert 'tool_panel_section' not in metadata, f'Tool panel section incorrectly found in metadata: {metadata}'
 
     def verify_installed_repository_data_table_entries(self, required_data_table_entries):
@@ -1582,7 +1582,7 @@ def verify_tool_metadata_for_installed_repository(self, installed_repository, st
         if strings_not_displayed is None:
             strings_not_displayed = []
         repository_id = self.security.encode_id(installed_repository.id)
-        for tool in installed_repository.metadata['tools']:
+        for tool in installed_repository.metadata_['tools']:
             strings = list(strings_displayed)
             strings.extend([tool['id'], tool['description'], tool['version'], tool['guid'], tool['name']])
             params = dict(repository_id=repository_id, tool_id=tool['id'])
diff --git a/lib/tool_shed/test/functional/test_1070_invalid_tool.py b/lib/tool_shed/test/functional/test_1070_invalid_tool.py
index 3cc9ecf68da3..47c76e5a67ca 100644
--- a/lib/tool_shed/test/functional/test_1070_invalid_tool.py
+++ b/lib/tool_shed/test/functional/test_1070_invalid_tool.py
@@ -84,5 +84,5 @@ def test_0015_install_freebayes_repository(self):
                                                       strings_not_displayed=['bisulfite mapper'])
         self.verify_tool_metadata_for_installed_repository(installed_repository)
         self.update_installed_repository(installed_repository, strings_displayed=["there are no updates available"])
-        assert 'invalid_tools' in installed_repository.metadata, 'No invalid tools were defined in %s.' % \
+        assert 'invalid_tools' in installed_repository.metadata_, 'No invalid tools were defined in %s.' % \
             installed_repository.name
diff --git a/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py b/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py
index 89f994a3ee41..17178d96cc28 100644
--- a/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py
+++ b/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py
@@ -441,7 +441,7 @@ def test_9905_reset_metadata_on_all_repositories(self):
         repository_metadata = dict()
         repositories = self.test_db_util.get_all_installed_repositories(actually_installed=True)
         for repository in repositories:
-            repository_metadata[self.security.encode_id(repository.id)] = repository.metadata
+            repository_metadata[self.security.encode_id(repository.id)] = repository.metadata_
         self.reset_metadata_on_selected_installed_repositories(list(repository_metadata.keys()))
         for repository in repositories:
             self.test_db_util.ga_refresh(repository)
@@ -452,7 +452,7 @@ def test_9905_reset_metadata_on_all_repositories(self):
             # is normal and expected behavior, the functional tests assume that repository metadata will not change
             # in any way after a reset. A workaround is to remove the tool panel section from the stored repository
             # metadata dict, in order to eliminate the misleading detection of changed metadata.
-            if 'tool_panel_section' in old_metadata and 'tool_panel_section' not in repository.metadata:
+            if 'tool_panel_section' in old_metadata and 'tool_panel_section' not in repository.metadata_:
                 del old_metadata['tool_panel_section']
-            assert repository.metadata == old_metadata, 'Metadata for %s repository %s changed after reset. \nOld: %s\nNew: %s' % \
-                (repository.status, repository.name, old_metadata, repository.metadata)
+            assert repository.metadata_ == old_metadata, 'Metadata for %s repository %s changed after reset. \nOld: %s\nNew: %s' % \
+                (repository.status, repository.name, old_metadata, repository.metadata_)
diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py
index cdfa1c727d14..3e3c222b70e2 100644
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -175,7 +175,7 @@ def get_requirements_from_repository(repository):
     if not repository.includes_tools:
         return {}
     else:
-        return get_requirements_from_tools(repository.metadata.get('tools', []))
+        return get_requirements_from_tools(repository.metadata_.get('tools', []))
 
 
 def get_repository_categories(app, id):