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Move RepositoryMetadata out of mapping.py
Do not remap declaratively. The model contains '.metadata' attr; a declaratively-mapped class cannot have a .metadata attribute (it is used by SQLAlchemy's DeclarativeBase). Given that TS is currently (mostly) in maintenance code, it is reasonable to leave this as is rather than handle all references to this attribute in the codebase.
This commit is contained in:
Sergey Golitsynskiy
@@ -17,6 +17,7 @@ from sqlalchemy import (
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Integer,
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not_,
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String,
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Table,
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TEXT,
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true,
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UniqueConstraint,
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@@ -48,8 +49,6 @@ log = logging.getLogger(__name__)
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WEAK_HG_REPO_CACHE: Mapping['Repository', Any] = weakref.WeakKeyDictionary()
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if TYPE_CHECKING:
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from sqlalchemy.schema import Table
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class _HasTable:
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table: Table
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else:
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@@ -533,50 +532,6 @@ class Repository(Base, Dictifiable, _HasTable):
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return rval
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class RepositoryMetadata(Dictifiable, _HasTable):
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dict_collection_visible_keys = ['id', 'repository_id', 'numeric_revision', 'changeset_revision', 'malicious', 'downloadable', 'missing_test_components',
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'has_repository_dependencies', 'includes_datatypes', 'includes_tools', 'includes_tool_dependencies',
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'includes_tools_for_display_in_tool_panel', 'includes_workflows']
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dict_element_visible_keys = ['id', 'repository_id', 'numeric_revision', 'changeset_revision', 'malicious', 'downloadable', 'missing_test_components',
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'has_repository_dependencies', 'includes_datatypes', 'includes_tools', 'includes_tool_dependencies',
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'includes_tools_for_display_in_tool_panel', 'includes_workflows', 'repository_dependencies']
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def __init__(self, id=None, repository_id=None, numeric_revision=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False,
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downloadable=False, missing_test_components=None, tools_functionally_correct=False, test_install_error=False,
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has_repository_dependencies=False, includes_datatypes=False, includes_tools=False, includes_tool_dependencies=False,
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includes_workflows=False):
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self.id = id
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self.repository_id = repository_id
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self.numeric_revision = numeric_revision
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self.changeset_revision = changeset_revision
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self.metadata = metadata
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self.tool_versions = tool_versions
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self.malicious = malicious
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self.downloadable = downloadable
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self.missing_test_components = missing_test_components
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self.has_repository_dependencies = has_repository_dependencies
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# We don't consider the special case has_repository_dependencies_only_if_compiling_contained_td here.
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self.includes_datatypes = includes_datatypes
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self.includes_tools = includes_tools
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self.includes_tool_dependencies = includes_tool_dependencies
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self.includes_workflows = includes_workflows
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@property
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def includes_tools_for_display_in_tool_panel(self):
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if self.metadata:
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tool_dicts = self.metadata.get('tools', [])
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for tool_dict in tool_dicts:
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if tool_dict.get('add_to_tool_panel', True):
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return True
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return False
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@property
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def repository_dependencies(self):
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if self.has_repository_dependencies:
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return [repository_dependency for repository_dependency in self.metadata['repository_dependencies']['repository_dependencies']]
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return []
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class RepositoryReview(Base, Dictifiable, _HasTable):
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__tablename__ = 'repository_review'
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@@ -753,6 +708,86 @@ class Tag(Base, _HasTable):
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return "Tag(id=%s, type=%i, parent_id=%s, name=%s)" % (self.id, self.type, self.parent_id, self.name)
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# The RepositoryMetadata model is mapped imperatively (for details see discussion in PR #12064).
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# TLDR: a declaratively-mapped class cannot have a .metadata attribute (it is used by SQLAlchemy's DeclarativeBase).
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class RepositoryMetadata(Dictifiable, _HasTable):
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# Once the class has been mapped, all Column items in this table will be available
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# as instrumented class attributes on RepositoryMetadata.
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table = Table('repository_metadata', mapper_registry.metadata,
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Column('id', Integer, primary_key=True),
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Column('create_time', DateTime, default=now),
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Column('update_time', DateTime, default=now, onupdate=now),
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Column('repository_id', Integer, ForeignKey('repository.id'), index=True),
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Column('changeset_revision', TrimmedString(255), index=True),
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Column('numeric_revision', Integer, index=True),
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Column('metadata', MutableJSONType, nullable=True),
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Column('tool_versions', MutableJSONType, nullable=True),
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Column('malicious', Boolean, default=False),
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Column('downloadable', Boolean, default=True),
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Column('missing_test_components', Boolean, default=False, index=True),
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Column('has_repository_dependencies', Boolean, default=False, index=True),
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Column('includes_datatypes', Boolean, default=False, index=True),
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Column('includes_tools', Boolean, default=False, index=True),
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Column('includes_tool_dependencies', Boolean, default=False, index=True),
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Column('includes_workflows', Boolean, default=False, index=True))
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dict_collection_visible_keys = ['id', 'repository_id', 'numeric_revision', 'changeset_revision', 'malicious', 'downloadable', 'missing_test_components',
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'has_repository_dependencies', 'includes_datatypes', 'includes_tools', 'includes_tool_dependencies',
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'includes_tools_for_display_in_tool_panel', 'includes_workflows']
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dict_element_visible_keys = ['id', 'repository_id', 'numeric_revision', 'changeset_revision', 'malicious', 'downloadable', 'missing_test_components',
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'has_repository_dependencies', 'includes_datatypes', 'includes_tools', 'includes_tool_dependencies',
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'includes_tools_for_display_in_tool_panel', 'includes_workflows', 'repository_dependencies']
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def __init__(self, id=None, repository_id=None, numeric_revision=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False,
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downloadable=False, missing_test_components=None, tools_functionally_correct=False, test_install_error=False,
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has_repository_dependencies=False, includes_datatypes=False, includes_tools=False, includes_tool_dependencies=False,
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includes_workflows=False):
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self.id = id
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self.repository_id = repository_id
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self.numeric_revision = numeric_revision
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self.changeset_revision = changeset_revision
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self.metadata = metadata
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self.tool_versions = tool_versions
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self.malicious = malicious
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self.downloadable = downloadable
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self.missing_test_components = missing_test_components
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self.has_repository_dependencies = has_repository_dependencies
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# We don't consider the special case has_repository_dependencies_only_if_compiling_contained_td here.
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self.includes_datatypes = includes_datatypes
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self.includes_tools = includes_tools
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self.includes_tool_dependencies = includes_tool_dependencies
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self.includes_workflows = includes_workflows
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@property
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def includes_tools_for_display_in_tool_panel(self):
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if self.metadata:
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tool_dicts = self.metadata.get('tools', [])
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for tool_dict in tool_dicts:
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if tool_dict.get('add_to_tool_panel', True):
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return True
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return False
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@property
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def repository_dependencies(self):
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if self.has_repository_dependencies:
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return [repository_dependency for repository_dependency in self.metadata['repository_dependencies']['repository_dependencies']]
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return []
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# After the map_imperatively statement has been executed, the members of the
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# properties dictionary (repository, reviews) will be available as instrumented
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# class attributes on RepositoryMetadata.
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mapper_registry.map_imperatively(RepositoryMetadata, RepositoryMetadata.table, properties=dict(
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repository=relationship(Repository, back_populates='metadata_revisions'),
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reviews=relationship(RepositoryReview,
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viewonly=True,
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foreign_keys=lambda: [RepositoryReview.repository_id, RepositoryReview.changeset_revision], # type: ignore
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primaryjoin=lambda: ((RepositoryReview.repository_id == RepositoryMetadata.repository_id) # type: ignore
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& (RepositoryReview.changeset_revision == RepositoryMetadata.changeset_revision)), # type: ignore
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back_populates='repository_metadata')))
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# Utility methods
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def sort_by_attr(seq, attr):
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"""
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@@ -4,51 +4,17 @@ are encapsulated here.
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"""
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import logging
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from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, Table
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from sqlalchemy.orm import relation
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import tool_shed.webapp.model
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import tool_shed.webapp.util.shed_statistics as shed_statistics
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from galaxy.model.base import SharedModelMapping
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from galaxy.model.custom_types import MutableJSONType, TrimmedString
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from galaxy.model.orm.engine_factory import build_engine
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from galaxy.model.orm.now import now
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from tool_shed.webapp.model import mapper_registry
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from tool_shed.webapp.model import Repository
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from tool_shed.webapp.model import RepositoryMetadata
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from tool_shed.webapp.model import RepositoryReview
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from tool_shed.webapp.security import CommunityRBACAgent
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log = logging.getLogger(__name__)
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metadata = mapper_registry.metadata
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RepositoryMetadata.table = Table("repository_metadata", metadata,
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Column("id", Integer, primary_key=True),
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Column("create_time", DateTime, default=now),
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Column("update_time", DateTime, default=now, onupdate=now),
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Column("repository_id", Integer, ForeignKey("repository.id"), index=True),
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Column("changeset_revision", TrimmedString(255), index=True),
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Column("numeric_revision", Integer, index=True),
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Column("metadata", MutableJSONType, nullable=True),
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Column("tool_versions", MutableJSONType, nullable=True),
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Column("malicious", Boolean, default=False),
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Column("downloadable", Boolean, default=True),
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Column("missing_test_components", Boolean, default=False, index=True),
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Column("has_repository_dependencies", Boolean, default=False, index=True),
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Column("includes_datatypes", Boolean, default=False, index=True),
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Column("includes_tools", Boolean, default=False, index=True),
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Column("includes_tool_dependencies", Boolean, default=False, index=True),
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Column("includes_workflows", Boolean, default=False, index=True))
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mapper_registry.map_imperatively(RepositoryMetadata, RepositoryMetadata.table, properties=dict(
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repository=relation(Repository, back_populates='metadata_revisions'),
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reviews=relation(RepositoryReview,
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viewonly=True,
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foreign_keys=[RepositoryReview.repository_id, RepositoryReview.changeset_revision],
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primaryjoin=((RepositoryReview.repository_id == RepositoryMetadata.table.c.repository_id) & (RepositoryReview.changeset_revision == RepositoryMetadata.table.c.changeset_revision)),
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back_populates='repository_metadata')))
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class ToolShedModelMapping(SharedModelMapping):
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security_agent: CommunityRBACAgent
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