def create_repo(session, changeset, installed_changeset, config_filename=None): metadata = { 'tools': [{ 'add_to_tool_panel': False, # to have repository.includes_tools_for_display_in_tool_panel=False in InstalledRepositoryManager.activate_repository() 'guid': "github.com/galaxyproject/example/test_tool/0.%s" % changeset, 'tool_config': 'tool.xml' }], } if config_filename: metadata['shed_config_filename'] = config_filename repository = tool_shed_install.ToolShedRepository(metadata_=metadata) repository.tool_shed = "github.com" repository.owner = "galaxyproject" repository.name = "example" repository.changeset_revision = str(changeset) repository.installed_changeset_revision = str(installed_changeset) repository.deleted = False repository.uninstalled = False session.add(repository) session.flush() tool_dependency = tool_shed_install.ToolDependency( name='Name', version='100', type='package', status='ok', tool_shed_repository_id=repository.id, ) session.add(tool_dependency) return repository
def _repo_install(self, changeset): repository = tool_shed_install.ToolShedRepository() repository.tool_shed = "github.com" repository.owner = "galaxyproject" repository.name = "example" repository.changeset_revision = changeset repository.installed_changeset_revision = changeset repository.deleted = False repository.uninstalled = False self.app.install_model.context.add(repository) self.app.install_model.context.flush() return repository
def _repo_install(self, changeset, config_filename=None): metadata = {} if config_filename: metadata['shed_config_filename'] = config_filename repository = tool_shed_install.ToolShedRepository(metadata=metadata) repository.tool_shed = "github.com" repository.owner = "galaxyproject" repository.name = "example" repository.changeset_revision = changeset repository.installed_changeset_revision = changeset repository.deleted = False repository.uninstalled = False self.app.install_model.context.add(repository) self.app.install_model.context.flush() return repository
def _repo_install(self, changeset, config_filename=None): metadata = { 'tools': [{ 'add_to_tool_panel': False, # to have repository.includes_tools_for_display_in_tool_panel=False in InstalledRepositoryManager.activate_repository() 'guid': "github.com/galaxyproject/example/test_tool/0.%s" % changeset, 'tool_config': 'tool.xml' }], } if config_filename: metadata['shed_config_filename'] = config_filename 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 repository.changeset_revision = changeset repository.installed_changeset_revision = changeset repository.deleted = False repository.uninstalled = False self.app.install_model.context.add(repository) self.app.install_model.context.flush() return repository
def create_repo(app, changeset, installed_changeset, config_filename=None): metadata = { 'tools': [{ 'add_to_tool_panel': False, # to have repository.includes_tools_for_display_in_tool_panel=False in InstalledRepositoryManager.activate_repository() 'guid': "github.com/galaxyproject/example/test_tool/0.%s" % changeset, 'tool_config': 'tool.xml' }], } if config_filename: metadata['shed_config_filename'] = config_filename repository = tool_shed_install.ToolShedRepository(metadata=metadata) repository.tool_shed = "github.com" repository.owner = "galaxyproject" repository.name = "example" repository.changeset_revision = str(changeset) repository.installed_changeset_revision = str(installed_changeset) repository.deleted = False repository.uninstalled = False app.install_model.context.add(repository) return repository
def test_serialization(): repository = tool_shed_install.ToolShedRepository( owner="devteam", name="tophat", installed_changeset_revision="abcdefghijk", ) dependency = tool_shed_install.ToolDependency( name="tophat", version="2.0", type="package", status=tool_shed_install.ToolDependency.installation_status.INSTALLED, ) dependency.tool_shed_repository = repository tool_requirement = requirements.ToolRequirement( name="tophat", version="2.0", type="package", ) descript = dependencies.DependenciesDescription( requirements=[tool_requirement], installed_tool_dependencies=[dependency], ) result_descript = dependencies.DependenciesDescription.from_dict( descript.to_dict()) result_requirement = result_descript.requirements[0] assert result_requirement.name == "tophat" assert result_requirement.version == "2.0" assert result_requirement.type == "package" result_tool_shed_dependency = result_descript.installed_tool_dependencies[ 0] result_tool_shed_dependency.name = "tophat" result_tool_shed_dependency.version = "2.0" result_tool_shed_dependency.type = "package" result_tool_shed_repository = result_tool_shed_dependency.tool_shed_repository result_tool_shed_repository.name = "tophat" result_tool_shed_repository.owner = "devteam" result_tool_shed_repository.installed_changeset_revision = "abcdefghijk"