mirror of
https://github.com/Novartis/cellxgene-gateway.git
synced 2026-09-24 09:38:12 +08:00
Alok Saldanha
c03098af17
Due to issue with opening annotation files with "-" in the name, this doesn't quite work.
61 lines
2.4 KiB
Python
61 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 os
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import logging
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import socket
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cellxgene_location = os.environ.get("CELLXGENE_LOCATION")
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cellxgene_data = os.environ.get("CELLXGENE_DATA")
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gateway_port = int(os.environ.get("GATEWAY_PORT", "5005"))
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external_host = os.environ.get("EXTERNAL_HOST", os.environ.get("GATEWAY_HOST", f"localhost:{gateway_port}"))
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external_protocol = os.environ.get("EXTERNAL_PROTOCOL", os.environ.get("GATEWAY_PROTOCOL", "http"))
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ip = os.environ.get("GATEWAY_IP")
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extra_scripts = os.environ.get("GATEWAY_EXTRA_SCRIPTS")
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ttl = os.environ.get("GATEWAY_TTL")
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enable_upload = os.environ.get("GATEWAY_ENABLE_UPLOAD", "").lower() in ['true', '1']
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enable_annotations = os.environ.get("GATEWAY_ENABLE_ANNOTATIONS", "").lower() in ['true', '1']
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env_vars = {
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"CELLXGENE_LOCATION": cellxgene_location,
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"CELLXGENE_DATA": cellxgene_data,
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"GATEWAY_IP": ip,
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}
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optional_env_vars = {
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"EXTERNAL_HOST": external_host,
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"EXTERNAL_PROTOCOL": external_protocol,
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"GATEWAY_PORT": gateway_port,
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"GATEWAY_EXTRA_SCRIPTS": extra_scripts,
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"GATEWAY_TTL": ttl,
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"GATEWAY_ENABLE_UPLOAD": enable_upload,
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"GATEWAY_ENABLE_ANNOTATIONS": enable_annotations,
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}
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def validate():
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if not all(env_vars.values()):
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raise ValueError(
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f"""
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Please ensure that environment variables are set correctly.
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The ones with None below are missing and need to be set.
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{env_vars}
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Set them at the terminal before running the gateway.
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An example is:
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export CELLXGENE_LOCATION=~/anaconda/envs/cellxgene-dev/bin/cellxgene
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export CELLXGENE_DATA=../cellxgene_data
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export GATEWAY_IP=127.0.0.1
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"""
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)
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else:
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logging.getLogger("cellxgene_gateway").info(f"Got required env: {env_vars}", )
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logging.getLogger("cellxgene_gateway").info(f"Got optional env: {optional_env_vars}")
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