Source code for yggdrasil.drivers.OSRModelDriver

import os
import git
import copy
import shutil
import subprocess
import tempfile
import logging
import chevron
import io as sio
import warnings
import xml.etree.ElementTree as ET
from yggdrasil import tools, platform
from yggdrasil.components import import_component
from yggdrasil.drivers.ExecutableModelDriver import ExecutableModelDriver
from yggdrasil.drivers.CPPModelDriver import CPPModelDriver


logger = logging.getLogger(__name__)


[docs]class OSRModelDriver(ExecutableModelDriver): r"""Class for running OpenSimRoot model. Args: sync_vars_in (list, optional): Variables that should be synchronized from other models. Defaults to []. sync_vars_out (list, optional): Variables that should be synchronized to other models. Defaults to []. copy_xml_to_osr (bool, optional): If True, the XML file(s) will be copied to the OSR repository InputFiles direcitory before running. This is necessary if the XML file(s) use any of the files located there since OSR always assumes the included file paths are relative. Defaults to False. update_interval (float, optional): Max simulation interval at which synchronization should occur (in days). Defaults to 1.0 if not provided. If the XML input file loads additional export modules that output at a shorter rate, the existing table of values will be extrapolated. """ _schema_subtype_description = 'Model is an OSR model.' _schema_properties = { 'sync_vars_in': {'type': 'array', 'items': {'type': 'string'}, 'default': []}, 'sync_vars_out': {'type': 'array', 'items': {'type': 'string'}, 'default': []}, 'copy_xml_to_osr': {'type': 'boolean', 'default': False}, 'update_interval': {'type': 'object', 'additionalProperties': {'type': 'float'}, 'default': {'timesync': 1.0}}} executable_type = 'dsl' language = 'osr' language_ext = '.xml' base_languages = ['cpp'] interface_dependencies = ['make'] repository = None executable_path = None repository_url = "https://gitlab.com/langmm/OpenSimRoot.git" repository_branch = "volatile_active" _config_keys = ['repository'] _config_attr_map = [{'attr': 'repository', 'key': 'repository'}]
[docs] @staticmethod def after_registration(cls, **kwargs): r"""Operations that should be performed to modify class attributes after registration. """ ExecutableModelDriver.after_registration(cls, **kwargs) if cls.repository is not None: if platform._is_win: # pragma: windows cls.executable_path = os.path.join( cls.repository, 'OpenSimRoot', 'StaticBuild_win64', 'OpenSimRootYgg') + '.exe' else: cls.executable_path = os.path.join( cls.repository, 'OpenSimRoot', 'StaticBuild', 'OpenSimRootYgg')
[docs] def parse_arguments(self, *args, **kwargs): r"""Sort model arguments to determine which one is the executable and which ones are arguments. Args: *args: Additional arguments are passed to the parent class's method. **kwargs: Additional keyword arguments are passed to the parent class's method. """ super(OSRModelDriver, self).parse_arguments(*args, **kwargs) self.model_file_orig = self.model_file self.model_file = '_copy'.join(os.path.splitext(self.model_file_orig)) if self.copy_xml_to_osr and (self.repository is not None): self.model_file = os.path.join( self.repository, 'OpenSimRoot', 'InputFiles', os.path.basename(self.model_file)) # if not (isinstance(self.executable_path, str) # and os.path.isfile(self.executable_path)): self.compile_dependencies() assert os.path.isfile(self.executable_path)
[docs] @classmethod def is_library_installed(cls, lib, **kwargs): r"""Determine if a dependency is installed. Args: lib (str): Name of the library that should be checked. **kwargs: Additional keyword arguments are ignored. Returns: bool: True if the library is installed, False otherwise. """ # Need to treat gnu make as dependency since OSR Makefile is not # compatible with nmake if lib == 'make': return bool(shutil.which('make')) return super(OSRModelDriver, cls).is_library_installed( lib, **kwargs) # pragma: debug
[docs] @classmethod def compile_dependencies(cls, target='OpenSimRootYgg', toolname=None): r"""Compile the OpenSimRoot executable with the yggdrasil flag set. Args: target (str, optional): Make target that should be build. Defaults to 'OpenSimRootYgg' (the yggdrasil-instrumented version of the OSR executable). toolname (str, optional): C++ compiler that should be used. Forced to be 'cl.exe' on windows. Otherwise the default C++ compiler will be used. """ if (cls.repository is not None) and CPPModelDriver.is_installed(): if not os.path.isdir(cls.repository): # pragma: debug # This will only need to be called if the tempdir was cleaned up cls.clone_repository(cls.repository) # toolname = CPPModelDriver.get_tool('compiler', # return_prop='name', # default=None) cwd = os.path.join(cls.repository, 'OpenSimRoot') flags = ['-j4'] env = copy.deepcopy(os.environ) if platform._is_win: # pragma: windows toolname = 'cl' env['YGG_OSR_TOOL'] = toolname if toolname == 'cl': cl_path = shutil.which(toolname + '.exe') if cl_path: msvc_bin = os.path.dirname(cl_path) env['YGG_OSR_CXX'] = cl_path env['YGG_OSR_LINK'] = os.path.join(msvc_bin, 'link.exe') for k in ['CL', '_CL_']: v = os.environ.get(k, None) if v is not None: # pragma: appveyor env[k] = v.replace('/', '-').replace('\\', '/') else: # pragma: debug env.pop('YGG_OSR_TOOL') warnings.warn( "The MSVC compiler is not installed. Be aware " "that the GNU compiler takes a *very* long time " "to compile OpenSimRoot against yggdrasil on " "Windows (> 1 hr).") cwd = os.path.join(cwd, 'StaticBuild_win64') else: cwd = os.path.join(cwd, 'StaticBuild') if target != 'cleanygg': for x in cls.base_languages: base_cls = import_component('model', x) base_cls.compile_dependencies(toolname=toolname) elif not os.path.isfile(cls.executable_path): return cmd = ['make', target] + flags subprocess.check_call(cmd, cwd=cwd, env=env)
[docs] def write_wrappers(self, **kwargs): r"""Write any wrappers needed to compile and/or run a model. Args: **kwargs: Keyword arguments are passed to the parent class's method. Returns: list: Full paths to any created wrappers. """ out = super(OSRModelDriver, self).write_wrappers(**kwargs) out.append(self.wrap_xml(self.model_file_orig, self.model_file)) return out
[docs] def wrap_xml(self, src, dst): r"""Wrap the input XML, adding tags for the inputs/outputs specified for this model. Args: src (str): Full path to the XML file that should be wrapped. dst (str): Full path to the location where the updated XML should be saved. Returns: str: Full path to XML file produced. """ with open(src, 'r') as fd: src_contents = fd.read() src_contents = chevron.render( sio.StringIO(src_contents).getvalue(), self.set_env()) root = ET.fromstring(src_contents) timesync = self.timesync assert timesync if not isinstance(timesync, list): timesync = [timesync] for tsync in reversed(timesync): ivars = tsync.get('inputs', []) ovars = tsync.get('outputs', []) assert isinstance(ivars, list) assert isinstance(ovars, list) ivars = ' '.join(ivars) ovars = ' '.join(ovars) tupdate = self.update_interval.get(tsync['name'], 1.0) cask = ET.Element('SimulaCask', attrib={'name': tsync['name'], 'interval': str(tupdate)}) if ivars: icask = ET.Element('SimulaCaskInputs') icask.text = ivars cask.insert(-1, icask) if ovars: ocask = ET.Element('SimulaCaskOutputs') ocask.text = ovars cask.insert(-1, ocask) probe = ET.Element("SimulaBase", name="probeCaskObjects") probe_vals = [ET.Element("SimulaConstant", name="run", type="bool"), ET.Element("SimulaConstant", name="timeInterval", type="time"), ET.Element("SimulaConstant", name="requestedVariables", type="string")] probe_vals[0].text = '1' probe_vals[1].text = str(tupdate) probe_vals[2].text = ', '.join(ivars.split()) probe.extend(probe_vals) probe_directive = ET.Element( 'SimulaDirective', attrib={'path': "/simulationControls/outputParameters"}) probe_directive.append(probe) root.extend([cask, probe_directive]) tree = ET.ElementTree(root) tree.write(dst) return dst
[docs] @classmethod def is_language_installed(cls): r"""Determine if the interpreter/compiler for the associated programming language is installed. Returns: bool: True if the language interpreter/compiler is installed. """ return (cls.repository is not None)
[docs] @classmethod def clone_repository(cls, dest=None): r"""Clone the OpenSimRoot repository. Args: dest (str, optional): Full path to location where the repository should be cloned. Defaults to '$TEMP/OpenSimRoot'. Returns: str: Full path to location where the repository was cloned. """ if dest is None: dest = os.path.join(tempfile.gettempdir(), 'OpenSimRoot') if not os.path.isdir(dest): # pragma: config repo = git.Repo.clone_from(cls.repository_url, dest, branch=cls.repository_branch) repo.close() return dest
[docs] @classmethod def configure_executable_type(cls, cfg): r"""Add configuration options specific in the executable type before the libraries are configured. Args: cfg (CisConfigParser): Config class that options should be set for. Returns: list: Section, option, description tuples for options that could not be set. """ # TODO: Move clone + compile to install out = super(OSRModelDriver, cls).configure_executable_type(cfg) opt = 'repository' desc = 'The full path to the OpenSimRoot repository.' # if platform._is_win: # pragma: windows # out.append((cls.language, opt, desc)) # return out if (((not cfg.has_option(cls.language, opt)) or (not os.path.isdir(cfg.get(cls.language, opt))))): fname = 'OpenSimRoot' fpath = tools.locate_file(fname) if not fpath: logger.info('Could not locate %s, attempting to clone' % fname) try: fpath = cls.clone_repository() except BaseException as e: # pragma: debug logger.info('Failed to clone from %s. error = %s' % (cls.repository_url, str(e))) out.append((cls.language, opt, desc)) if fpath: logger.info('Located %s: %s' % (fname, fpath)) cfg.set(cls.language, opt, fpath) return out
[docs] @classmethod def set_env_class(cls, **kwargs): r"""Set environment variables that are instance independent. Args: **kwargs: Additional keyword arguments are passed to the parent class's method. Returns: dict: Environment variables for the model process. """ out = super(OSRModelDriver, cls).set_env_class(**kwargs) if cls.repository is not None: out['OSR_REPOSITORY'] = cls.repository kwargs['existing'] = out out = CPPModelDriver.set_env_class(**kwargs) return out
[docs] @classmethod def language_executable(cls, **kwargs): r"""Command required to compile/run a model written in this language from the command line. Returns: str: Name of (or path to) compiler/interpreter executable required to run the compiler/interpreter from the command line. """ return cls.executable_path
[docs] @classmethod def executable_command(cls, args, **kwargs): r"""Compose a command for running a program using the exectuable for this language (compiler/interpreter) with the provided arguments. Args: args (list): The program that returned command should run and any arguments that should be provided to it. unused_kwargs (dict, optional): Existing dictionary that unused keyword arguments should be added to. Defaults to None and is ignored. **kwargs: Additional keyword arguments are passed to the parent class. Returns: list: Arguments composing the command required to run the program from the command line using the executable for this language. """ args = [cls.language_executable()] + args return super(OSRModelDriver, cls).executable_command(args, **kwargs)
[docs] @classmethod def cleanup_dependencies(cls, *args, **kwargs): r"""Cleanup dependencies.""" cls.compile_dependencies(target='cleanygg') super(OSRModelDriver, cls).cleanup_dependencies(*args, **kwargs)
[docs] @classmethod def get_testing_options(cls): r"""Method to return a dictionary of testing options for this class. Returns: dict: Dictionary of variables to use for testing. Key/value pairs: kwargs (dict): Keyword arguments for driver instance. deps (list): Dependencies to install. """ out = super(OSRModelDriver, cls).get_testing_options() out['kwargs'].update( timesync={'name': 'timesync', 'inputs': ['carbonAllocation2Roots'], 'outputs': ['carbonAllocation2Roots']}, copy_xml_to_osr=True) out['requires_partner'] = True return out