Merge pull request #12756 from ic4f/dev_install_model_declarative

Convert install_model to declarative mapping

lib/galaxy/model/tool_shed_install/__init__.py

@@ -3,24 +3,81 @@
 from enum import Enum
 from typing import TYPE_CHECKING
 
+from sqlalchemy import (
+    Boolean,
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    String,
+    Table,
+    TEXT,
+)
+from sqlalchemy.orm import (
+    registry,
+    relationship,
+)
+from sqlalchemy.orm.decl_api import DeclarativeMeta
+
+from galaxy.model.custom_types import (
+    MutableJSONType,
+    TrimmedString
+)
+from galaxy.model.orm.now import now
 from galaxy.util import asbool
 from galaxy.util.bunch import Bunch
 from galaxy.util.dictifiable import Dictifiable
 from galaxy.util.tool_shed import common_util
 
 log = logging.getLogger(__name__)
 
+mapper_registry = registry()
 
 if TYPE_CHECKING:
-    from sqlalchemy.schema import Table
-
     class _HasTable:
         table: Table
 else:
     _HasTable = object
 
 
-class ToolShedRepository(_HasTable):
+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(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',
@@ -46,7 +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
@@ -57,7 +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
@@ -96,11 +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):
         """
@@ -125,7 +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']
@@ -158,11 +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:
@@ -174,7 +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:
@@ -190,28 +247,28 @@ 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
         return False
 
     @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):
@@ -350,7 +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 = \
@@ -447,7 +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:
@@ -484,20 +541,49 @@ 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(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')
 
     def __init__(self, tool_shed_repository_id=None, repository_dependency_id=None):
         self.tool_shed_repository_id = tool_shed_repository_id
         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(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
 
 
-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(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)
+    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
     installation_status = Bunch(NEVER_INSTALLED='Never installed',
@@ -568,14 +654,21 @@ def is_installed(self):
         return self.status == self.installation_status.INSTALLED
 
 
-class ToolVersion(Dictifiable, _HasTable):
-    dict_element_visible_keys = ['id', 'tool_shed_repository']
+class ToolVersion(Base, Dictifiable, _HasTable):
+    __tablename__ = 'tool_version'
 
-    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
+    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(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
+    tool_shed_repository = relationship('ToolShedRepository', back_populates='tool_versions')
+
+    dict_element_visible_keys = ['id', 'tool_shed_repository']
 
     def to_dict(self, view='element'):
         rval = super().to_dict(view=view)
@@ -587,17 +680,9 @@ def to_dict(self, view='element'):
         return rval
 
 
-class ToolVersionAssociation(_HasTable):
-
-    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 ToolVersionAssociation(Base, _HasTable):
+    __tablename__ = 'tool_version_association'
 
-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
+    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)