mirror of
https://github.com/Novartis/cellxgene-gateway.git
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94 lines
3.6 KiB
Python
94 lines
3.6 KiB
Python
# Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed
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# under the Apache License, Version 2.0 (the "License"); you may not use
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# this file except in compliance with the License. You may obtain a copy
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# of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless
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# required by applicable law or agreed to in writing, software distributed
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# under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
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# OR CONDITIONS OF ANY KIND, either express or implied. See the License for
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# the specific language governing permissions and limitations under the License.
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import logging
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import subprocess
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from http import HTTPStatus
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from cellxgene_gateway.cache_entry import CacheEntryStatus
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from cellxgene_gateway.dir_util import make_annotations
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from cellxgene_gateway.env import cellxgene_args, enable_annotations, enable_backed_mode
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from cellxgene_gateway.process_exception import ProcessException
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logger = logging.getLogger(__name__)
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class SubprocessBackend:
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def __init__(self):
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pass
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def create_cmd(self, cellxgene_loc, file_path, port, scripts, annotation_file_path):
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if enable_annotations and not annotation_file_path is None:
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if annotation_file_path == "":
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extra_args = f" --annotations-dir {make_annotations(file_path)}"
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else:
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extra_args = f" --annotations-file {annotation_file_path}"
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gene_sets_file_path = annotation_file_path[:-4] + "_gene_sets.csv"
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extra_args += f" --gene-sets-file {gene_sets_file_path}"
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else:
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extra_args = " --disable-annotations"
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extra_args += " --disable-gene-sets-save"
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if enable_backed_mode:
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extra_args += " --backed"
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if not cellxgene_args is None:
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extra_args += f" {cellxgene_args}"
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cmd = (
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f"yes | {cellxgene_loc} launch {file_path}"
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+ f" --port {port}"
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+ " --host 127.0.0.1"
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+ extra_args
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)
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for s in scripts:
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cmd += f" --scripts {s}"
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return cmd
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def launch(self, cellxgene_loc, scripts, cache_entry):
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cmd = self.create_cmd(
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cellxgene_loc,
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cache_entry.key.file_path,
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cache_entry.port,
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scripts,
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cache_entry.key.annotation_file_path,
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)
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logger.info(f"launching {cmd}")
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process = subprocess.Popen(
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[cmd], stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True
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)
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while True:
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output = process.stdout.readline().decode()
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if output == "[cellxgene] Type CTRL-C at any time to exit.\n":
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break
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elif output == "":
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stderr = process.stderr.read().decode()
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if (
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"Error while loading file" in stderr
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or "Could not open file" in stderr
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):
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message = "File was invalid."
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http_status = HTTPStatus.BAD_REQUEST
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else:
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message = "Cellxgene failed to launch dataset."
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http_status = HTTPStatus.INTERNAL_SERVER_ERROR
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cache_entry.status = CacheEntryStatus.error
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cache_entry.set_error(message, stderr, http_status)
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raise ProcessException.from_cache_entry(cache_entry)
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else:
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cache_entry.append_output(output)
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cache_entry.set_loaded(process.pid)
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for output in process.communicate():
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logger.debug(f"cellxgene:{output}")
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logger.info(f"exiting {cmd}")
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