mirror of
https://github.com/Novartis/cellxgene-gateway.git
synced 2026-09-22 19:38:11 +08:00
Alok Saldanha
c03098af17
Due to issue with opening annotation files with "-" in the name, this doesn't quite work.
78 lines
2.4 KiB
Python
78 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 time
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from threading import Thread
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from flask_api import status
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from cellxgene_gateway import env
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from cellxgene_gateway.cache_entry import CacheEntry
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from cellxgene_gateway.cellxgene_exception import CellxgeneException
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from cellxgene_gateway.subprocess_backend import SubprocessBackend
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process_backend = SubprocessBackend()
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def is_port_in_use(port):
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import socket
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with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
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return s.connect_ex(('localhost', port)) == 0
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class BackendCache:
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def __init__(self):
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self.entry_list = []
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def get_ports(self):
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contents = self.entry_list
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return [c.port for c in contents]
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def check_entry(self, key):
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contents = self.entry_list
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matches = [
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c
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for c in contents
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if c.key.dataset == key.dataset and c.key.annotation_file == key.annotation_file and c.status != "terminated"
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]
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if len(matches) == 0:
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return None
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elif len(matches) == 1:
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return matches[0]
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else:
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raise CellxgeneException(
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status.HTTP_500_INTERNAL_SERVER_ERROR,
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"Found " + str(len(matches)) + " for " + dataset,
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)
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def create_entry(self, key, scripts):
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port = 8000
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existing_ports = self.get_ports()
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while (port in existing_ports) or is_port_in_use(port):
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port += 1
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entry = CacheEntry.for_key(key, port)
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background_thread = Thread(
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target=process_backend.launch,
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args=(env.cellxgene_location, scripts, entry),
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)
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background_thread.start()
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self.entry_list.append(entry)
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time.sleep(1) # Automatic refresh is too fast, needs a second to pause
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return entry
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def prune(self, process):
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self.entry_list.remove(process)
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process.terminate()
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