runner.py 文件源码

def find_missing_tools(self, workflow=None):
        """
        Find tools required by the workflow to test and not installed on the configured Galaxy server.

        :type workflow: :class:`bioblend.galaxy.objects.wrappers.Workflow`
        :param workflow: an optional instance of :class:`bioblend.galaxy.objects.wrappers.Workflow`

        :rtype: list
        :return: the list of missing tools
        """
        _logger.debug("Checking required tools ...")
        workflow = self.get_galaxy_workflow() if not workflow else workflow
        available_tools = self._galaxy_instance.tools.list()
        missing_tools = []
        _logger.debug("Available tools: %s", ", ".join(["{0}, {1}".format(t.id, t.version) for t in available_tools]))
        for order, step in _iteritems(workflow.steps):
            if step.tool_id and len([t for t in available_tools
                                     if t.id == step.tool_id and t.version == step.tool_version]) == 0:
                missing_tools.append((step.tool_id, step.tool_version))
        _logger.debug("Missing tools: {0}".format("None"
                                                  if len(missing_tools) == 0
                                                  else ", ".join(["{0} (version {1})"
                                                                 .format(x[0], x[1]) for x in missing_tools])))
        _logger.debug("Checking required tools: DONE")
        return missing_tools