# Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed # under the Apache License, Version 2.0 (the "License"); you may not use # this file except in compliance with the License. You may obtain a copy # of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless # required by applicable law or agreed to in writing, software distributed # under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES # OR CONDITIONS OF ANY KIND, either express or implied. See the License for # the specific language governing permissions and limitations under the License. import logging import subprocess from flask_api import status from cellxgene_gateway.cache_entry import CacheEntryStatus from cellxgene_gateway.dir_util import make_annotations from cellxgene_gateway.path_util import get_annotation_file_path, get_file_path from cellxgene_gateway.env import ( enable_annotations, enable_backed_mode, cellxgene_args, ) from cellxgene_gateway.process_exception import ProcessException class SubprocessBackend: def __init__(self): pass def create_cmd( self, cellxgene_loc, file_path, port, scripts, annotation_file_path ): if enable_annotations and not annotation_file_path is None: if annotation_file_path == "": extra_args = ( f" --annotations-dir {make_annotations(file_path)}" ) else: extra_args = f" --annotations-file {annotation_file_path}" else: extra_args = " --disable-annotations" if enable_backed_mode: extra_args += " --backed" if not cellxgene_args is None: extra_args += f" {cellxgene_args}" cmd = ( f"yes | {cellxgene_loc} launch {file_path}" + " --port " + str(port) + " --host 127.0.0.1" + extra_args ) for s in scripts: cmd += f" --scripts {s}" return cmd def launch(self, cellxgene_loc, scripts, cache_entry): cmd = self.create_cmd( cellxgene_loc, get_file_path(cache_entry.key), cache_entry.port, scripts, get_annotation_file_path(cache_entry.key), ) logging.getLogger("cellxgene_gateway").info(f"launching {cmd}") process = subprocess.Popen( [cmd], stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True ) while True: output = process.stdout.readline().decode() if output == "[cellxgene] Type CTRL-C at any time to exit.\n": break elif output == "": stderr = process.stderr.read().decode() if ( "Error while loading file" in stderr or "Could not open file" in stderr ): message = "File was invalid." http_status = status.HTTP_400_BAD_REQUEST else: message = "Cellxgene failed to launch dataset." http_status = status.HTTP_500_INTERNAL_SERVER_ERROR cache_entry.status = CacheEntryStatus.error cache_entry.set_error(message, stderr, http_status) raise ProcessException.from_cache_entry(cache_entry) else: cache_entry.append_output(output) cache_entry.set_loaded(process.pid) return