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"
