def check(self, path_pairs): result = RepoCheckResult() for repo_path, system_path in path_pairs: LOG.debug('checking "{}" <-> "{}"...'.format(repo_path, system_path)) repo = Path(self.repo_path).joinpath(repo_path) system = Path(system_path) pair = RepoPathPair(repo, system) repo = repo.expanduser() system = system.expanduser() pair.update(repo, system) status = diffcheck(repo, system) LOG.debug('done, status: {}'.format(status)) pair.status = status result.add_pair(pair) return result
def gmx_mpi_linked(link): gmx_exe = distutils.spawn.find_executable('gmx') gmx_mpi = Path('~/gmx_mpi').expanduser() if not link: return '' else: gmx_mpi.symlink_to(gmx_exe) return str(gmx_mpi.expanduser())
def _resolve_attachment_path(self, path): """Find attachment file or raise MailmergeError.""" # Error on empty path if not path.strip(): raise MailmergeError("Empty attachment header.") # Create a Path object and handle home directory (tilde ~) notation path = Path(path.strip()) path = path.expanduser() # Relative paths are relative to the template's parent dir if not path.is_absolute(): path = self.template_path.parent / path # Resolve any symlinks path = path.resolve() # Check that the attachment exists if not path.exists(): raise MailmergeError("Attachment not found: {}".format(path)) return path
def upload_artifact(self, name, artifact_object=None, metadata=None, delete_after_upload=False): if not Session.check_min_api_version('2.3'): LoggerRoot.get_base_logger().warning( 'Artifacts not supported by your TRAINS-server version, ' 'please upgrade to the latest server version') return False if name in self._artifacts_container: raise ValueError( "Artifact by the name of {} is already registered, use register_artifact" .format(name)) artifact_type_data = tasks.ArtifactTypeData() override_filename_in_uri = None override_filename_ext_in_uri = None uri = None if np and isinstance(artifact_object, np.ndarray): artifact_type = 'numpy' artifact_type_data.content_type = 'application/numpy' artifact_type_data.preview = str(artifact_object.__repr__()) override_filename_ext_in_uri = '.npz' override_filename_in_uri = name + override_filename_ext_in_uri fd, local_filename = mkstemp(prefix=quote(name, safe="") + '.', suffix=override_filename_ext_in_uri) os.close(fd) np.savez_compressed(local_filename, **{name: artifact_object}) delete_after_upload = True elif pd and isinstance(artifact_object, pd.DataFrame): artifact_type = 'pandas' artifact_type_data.content_type = 'text/csv' artifact_type_data.preview = str(artifact_object.__repr__()) override_filename_ext_in_uri = self._save_format override_filename_in_uri = name fd, local_filename = mkstemp(prefix=quote(name, safe="") + '.', suffix=override_filename_ext_in_uri) os.close(fd) artifact_object.to_csv(local_filename, compression=self._compression) delete_after_upload = True elif isinstance(artifact_object, Image.Image): artifact_type = 'image' artifact_type_data.content_type = 'image/png' desc = str(artifact_object.__repr__()) artifact_type_data.preview = desc[1:desc.find(' at ')] override_filename_ext_in_uri = '.png' override_filename_in_uri = name + override_filename_ext_in_uri fd, local_filename = mkstemp(prefix=quote(name, safe="") + '.', suffix=override_filename_ext_in_uri) os.close(fd) artifact_object.save(local_filename) delete_after_upload = True elif isinstance(artifact_object, dict): artifact_type = 'JSON' artifact_type_data.content_type = 'application/json' preview = json.dumps(artifact_object, sort_keys=True, indent=4) override_filename_ext_in_uri = '.json' override_filename_in_uri = name + override_filename_ext_in_uri fd, local_filename = mkstemp(prefix=quote(name, safe="") + '.', suffix=override_filename_ext_in_uri) os.write(fd, bytes(preview.encode())) os.close(fd) artifact_type_data.preview = preview delete_after_upload = True elif isinstance(artifact_object, six.string_types) and urlparse( artifact_object).scheme in remote_driver_schemes: # we should not upload this, just register local_filename = None uri = artifact_object artifact_type = 'custom' artifact_type_data.content_type = mimetypes.guess_type( artifact_object)[0] elif isinstance(artifact_object, six.string_types + (Path, )): # check if single file artifact_object = Path(artifact_object) artifact_object.expanduser().absolute() try: create_zip_file = not artifact_object.is_file() except Exception: # Hack for windows pathlib2 bug, is_file isn't valid. create_zip_file = True else: # We assume that this is not Windows os if artifact_object.is_dir(): # change to wildcard artifact_object /= '*' if create_zip_file: folder = Path('').joinpath(*artifact_object.parts[:-1]) if not folder.is_dir() or not folder.parts: raise ValueError( "Artifact file/folder '{}' could not be found".format( artifact_object.as_posix())) wildcard = artifact_object.parts[-1] files = list(Path(folder).rglob(wildcard)) override_filename_ext_in_uri = '.zip' override_filename_in_uri = folder.parts[ -1] + override_filename_ext_in_uri fd, zip_file = mkstemp( prefix=quote(folder.parts[-1], safe="") + '.', suffix=override_filename_ext_in_uri) try: artifact_type_data.content_type = 'application/zip' artifact_type_data.preview = 'Archive content {}:\n'.format( artifact_object.as_posix()) with ZipFile(zip_file, 'w', allowZip64=True, compression=ZIP_DEFLATED) as zf: for filename in sorted(files): if filename.is_file(): relative_file_name = filename.relative_to( folder).as_posix() artifact_type_data.preview += '{} - {}\n'.format( relative_file_name, humanfriendly.format_size( filename.stat().st_size)) zf.write(filename.as_posix(), arcname=relative_file_name) except Exception as e: # failed uploading folder: LoggerRoot.get_base_logger().warning( 'Exception {}\nFailed zipping artifact folder {}'. format(folder, e)) return None finally: os.close(fd) artifact_object = zip_file artifact_type = 'archive' artifact_type_data.content_type = mimetypes.guess_type( artifact_object)[0] local_filename = artifact_object delete_after_upload = True else: if not artifact_object.is_file(): raise ValueError( "Artifact file '{}' could not be found".format( artifact_object.as_posix())) override_filename_in_uri = artifact_object.parts[-1] artifact_object = artifact_object.as_posix() artifact_type = 'custom' artifact_type_data.content_type = mimetypes.guess_type( artifact_object)[0] local_filename = artifact_object else: raise ValueError("Artifact type {} not supported".format( type(artifact_object))) # remove from existing list, if exists for artifact in self._task_artifact_list: if artifact.key == name: if artifact.type == self._pd_artifact_type: raise ValueError( "Artifact of name {} already registered, " "use register_artifact instead".format(name)) self._task_artifact_list.remove(artifact) break if not local_filename: file_size = None file_hash = None else: # check that the file to upload exists local_filename = Path(local_filename).absolute() if not local_filename.exists() or not local_filename.is_file(): LoggerRoot.get_base_logger().warning( 'Artifact upload failed, cannot find file {}'.format( local_filename.as_posix())) return False file_hash, _ = self.sha256sum(local_filename.as_posix()) file_size = local_filename.stat().st_size uri = self._upload_local_file( local_filename, name, delete_after_upload=delete_after_upload, override_filename=override_filename_in_uri, override_filename_ext=override_filename_ext_in_uri) timestamp = int(time()) artifact = tasks.Artifact( key=name, type=artifact_type, uri=uri, content_size=file_size, hash=file_hash, timestamp=timestamp, type_data=artifact_type_data, display_data=[(str(k), str(v)) for k, v in metadata.items()] if metadata else None) # update task artifacts with self._task_edit_lock: self._task_artifact_list.append(artifact) self._task.set_artifacts(self._task_artifact_list) return True
def upload_artifact(self, name, artifact_object=None, metadata=None, preview=None, delete_after_upload=False, auto_pickle=True): # type: (str, Optional[object], Optional[dict], Optional[str], bool, bool) -> bool if not Session.check_min_api_version('2.3'): LoggerRoot.get_base_logger().warning( 'Artifacts not supported by your TRAINS-server version, ' 'please upgrade to the latest server version') return False if name in self._artifacts_container: raise ValueError( "Artifact by the name of {} is already registered, use register_artifact" .format(name)) # cast preview to string if preview: preview = str(preview) # convert string to object if try is a file/folder (dont try to serialize long texts if isinstance(artifact_object, six.string_types) and len(artifact_object) < 2048: # noinspection PyBroadException try: artifact_path = Path(artifact_object) if artifact_path.exists(): artifact_object = artifact_path elif '*' in artifact_object or '?' in artifact_object: # hackish, detect wildcard in tr files folder = Path('').joinpath(*artifact_path.parts[:-1]) if folder.is_dir() and folder.parts: wildcard = artifact_path.parts[-1] if list(Path(folder).rglob(wildcard)): artifact_object = artifact_path except Exception: pass artifact_type_data = tasks.ArtifactTypeData() artifact_type_data.preview = '' override_filename_in_uri = None override_filename_ext_in_uri = None uri = None if np and isinstance(artifact_object, np.ndarray): artifact_type = 'numpy' artifact_type_data.content_type = 'application/numpy' artifact_type_data.preview = preview or str( artifact_object.__repr__()) override_filename_ext_in_uri = '.npz' override_filename_in_uri = name + override_filename_ext_in_uri fd, local_filename = mkstemp(prefix=quote(name, safe="") + '.', suffix=override_filename_ext_in_uri) os.close(fd) np.savez_compressed(local_filename, **{name: artifact_object}) delete_after_upload = True elif pd and isinstance(artifact_object, pd.DataFrame): artifact_type = 'pandas' artifact_type_data.content_type = 'text/csv' artifact_type_data.preview = preview or str( artifact_object.__repr__()) override_filename_ext_in_uri = self._save_format override_filename_in_uri = name fd, local_filename = mkstemp(prefix=quote(name, safe="") + '.', suffix=override_filename_ext_in_uri) os.close(fd) artifact_object.to_csv(local_filename, compression=self._compression) delete_after_upload = True elif isinstance(artifact_object, Image.Image): artifact_type = 'image' artifact_type_data.content_type = 'image/png' desc = str(artifact_object.__repr__()) artifact_type_data.preview = preview or desc[1:desc.find(' at ')] override_filename_ext_in_uri = '.png' override_filename_in_uri = name + override_filename_ext_in_uri fd, local_filename = mkstemp(prefix=quote(name, safe="") + '.', suffix=override_filename_ext_in_uri) os.close(fd) artifact_object.save(local_filename) delete_after_upload = True elif isinstance(artifact_object, dict): artifact_type = 'JSON' artifact_type_data.content_type = 'application/json' preview = preview or json.dumps( artifact_object, sort_keys=True, indent=4) override_filename_ext_in_uri = '.json' override_filename_in_uri = name + override_filename_ext_in_uri fd, local_filename = mkstemp(prefix=quote(name, safe="") + '.', suffix=override_filename_ext_in_uri) os.write(fd, bytes(preview.encode())) os.close(fd) if len(preview) < self.max_preview_size_bytes: artifact_type_data.preview = preview else: artifact_type_data.preview = '# full json too large to store, storing first {}kb\n{}'.format( self.max_preview_size_bytes // 1024, preview[:self.max_preview_size_bytes]) delete_after_upload = True elif isinstance(artifact_object, ( Path, pathlib_Path, ) if pathlib_Path is not None else (Path, )): # check if single file artifact_object = Path(artifact_object) artifact_object.expanduser().absolute() # noinspection PyBroadException try: create_zip_file = not artifact_object.is_file() except Exception: # Hack for windows pathlib2 bug, is_file isn't valid. create_zip_file = True else: # We assume that this is not Windows os if artifact_object.is_dir(): # change to wildcard artifact_object /= '*' if create_zip_file: folder = Path('').joinpath(*artifact_object.parts[:-1]) if not folder.is_dir() or not folder.parts: raise ValueError( "Artifact file/folder '{}' could not be found".format( artifact_object.as_posix())) wildcard = artifact_object.parts[-1] files = list(Path(folder).rglob(wildcard)) override_filename_ext_in_uri = '.zip' override_filename_in_uri = folder.parts[ -1] + override_filename_ext_in_uri fd, zip_file = mkstemp( prefix=quote(folder.parts[-1], safe="") + '.', suffix=override_filename_ext_in_uri) try: artifact_type_data.content_type = 'application/zip' archive_preview = 'Archive content {}:\n'.format( artifact_object.as_posix()) with ZipFile(zip_file, 'w', allowZip64=True, compression=ZIP_DEFLATED) as zf: for filename in sorted(files): if filename.is_file(): relative_file_name = filename.relative_to( folder).as_posix() archive_preview += '{} - {}\n'.format( relative_file_name, humanfriendly.format_size( filename.stat().st_size)) zf.write(filename.as_posix(), arcname=relative_file_name) except Exception as e: # failed uploading folder: LoggerRoot.get_base_logger().warning( 'Exception {}\nFailed zipping artifact folder {}'. format(folder, e)) return False finally: os.close(fd) artifact_type_data.preview = preview or archive_preview artifact_object = zip_file artifact_type = 'archive' artifact_type_data.content_type = mimetypes.guess_type( artifact_object)[0] local_filename = artifact_object delete_after_upload = True else: if not artifact_object.is_file(): raise ValueError( "Artifact file '{}' could not be found".format( artifact_object.as_posix())) override_filename_in_uri = artifact_object.parts[-1] artifact_type_data.preview = preview or '{} - {}\n'.format( artifact_object, humanfriendly.format_size(artifact_object.stat().st_size)) artifact_object = artifact_object.as_posix() artifact_type = 'custom' artifact_type_data.content_type = mimetypes.guess_type( artifact_object)[0] local_filename = artifact_object elif (isinstance(artifact_object, six.string_types) and len(artifact_object) < 4096 and urlparse(artifact_object).scheme in remote_driver_schemes): # we should not upload this, just register local_filename = None uri = artifact_object artifact_type = 'custom' artifact_type_data.content_type = mimetypes.guess_type( artifact_object)[0] elif isinstance(artifact_object, six.string_types): # if we got here, we should store it as text file. artifact_type = 'string' artifact_type_data.content_type = 'text/plain' if preview: artifact_type_data.preview = preview elif len(artifact_object) < self.max_preview_size_bytes: artifact_type_data.preview = artifact_object else: artifact_type_data.preview = '# full text too large to store, storing first {}kb\n{}'.format( self.max_preview_size_bytes // 1024, artifact_object[:self.max_preview_size_bytes]) delete_after_upload = True override_filename_ext_in_uri = '.txt' override_filename_in_uri = name + override_filename_ext_in_uri fd, local_filename = mkstemp(prefix=quote(name, safe="") + '.', suffix=override_filename_ext_in_uri) os.close(fd) # noinspection PyBroadException try: with open(local_filename, 'wt') as f: f.write(artifact_object) except Exception: # cleanup and raise exception os.unlink(local_filename) raise elif auto_pickle: # if we are here it means we do not know what to do with the object, so we serialize it with pickle. artifact_type = 'pickle' artifact_type_data.content_type = 'application/pickle' # noinspection PyBroadException try: artifact_type_data.preview = preview or str( artifact_object.__repr__())[:self.max_preview_size_bytes] except Exception: artifact_type_data.preview = preview or '' delete_after_upload = True override_filename_ext_in_uri = '.pkl' override_filename_in_uri = name + override_filename_ext_in_uri fd, local_filename = mkstemp(prefix=quote(name, safe="") + '.', suffix=override_filename_ext_in_uri) os.close(fd) # noinspection PyBroadException try: with open(local_filename, 'wb') as f: pickle.dump(artifact_object, f) except Exception: # cleanup and raise exception os.unlink(local_filename) raise else: raise ValueError("Artifact type {} not supported".format( type(artifact_object))) # remove from existing list, if exists for artifact in self._task_artifact_list: if artifact.key == name: if artifact.type == self._pd_artifact_type: raise ValueError( "Artifact of name {} already registered, " "use register_artifact instead".format(name)) self._task_artifact_list.remove(artifact) break if not local_filename: file_size = None file_hash = None else: # check that the file to upload exists local_filename = Path(local_filename).absolute() if not local_filename.exists() or not local_filename.is_file(): LoggerRoot.get_base_logger().warning( 'Artifact upload failed, cannot find file {}'.format( local_filename.as_posix())) return False file_hash, _ = self.sha256sum(local_filename.as_posix()) file_size = local_filename.stat().st_size uri = self._upload_local_file( local_filename, name, delete_after_upload=delete_after_upload, override_filename=override_filename_in_uri, override_filename_ext=override_filename_ext_in_uri) timestamp = int(time()) artifact = tasks.Artifact( key=name, type=artifact_type, uri=uri, content_size=file_size, hash=file_hash, timestamp=timestamp, type_data=artifact_type_data, display_data=[(str(k), str(v)) for k, v in metadata.items()] if metadata else None) # update task artifacts with self._task_edit_lock: self._task_artifact_list.append(artifact) self._task.set_artifacts(self._task_artifact_list) return True