mirror of
https://github.com/Novartis/cellxgene-gateway.git
synced 2026-09-15 12:47:59 +08:00
72 lines
2.4 KiB
Python
72 lines
2.4 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 flask_api import status
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from process_exception import ProcessException
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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):
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cmd = (
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f"yes | {cellxgene_loc} launch {file_path}"
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+ " --port "
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+ str(port)
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+ " --host 127.0.0.1"
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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, cache_entry.file_path, cache_entry.port, scripts
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)
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logging.getLogger("werkzeug").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 = status.HTTP_400_BAD_REQUEST
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else:
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message = "Cellxgene failed to launch dataset."
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http_status = status.HTTP_500_INTERNAL_SERVER_ERROR
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cache_entry.status = "error"
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cache_entry.set_error(message, stderr, http_status)
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raise ProcessException.from_pid_object(cache_entry)
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else:
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cache_entry.all_output += output
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cache_entry.set_loaded(process.pid)
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return
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