mirror of
https://github.com/chanzuckerberg/cellxgene.git
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fb61bd6e9c
This splits the backend into two parts: the local backend for desktop cellxgene and the AWS backend for hosted cellxgene. The local backend is in local_server while the hosted remains in server. The general idea is to copy everything from server to local_server, pull unneeded stuff out of local_server, and keep server as-is for this PR. Not touching server means all the infra and deployment code will continue working just as it did before so we can make those changes incrementally.
136 lines
4.0 KiB
Python
136 lines
4.0 KiB
Python
import yaml
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default_config = """
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server:
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app:
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verbose: false
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debug: false
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host: localhost
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port : null
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open_browser: false
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force_https: false
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flask_secret_key: null
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authentication:
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# The authentication types may be "none" or "session"
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# none: No authentication support, features like user_annotations must not be enabled.
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# session: A session based userid is automatically generated. (no params needed)
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type: session
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insecure_test_environment: false
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single_dataset:
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# If datapath is set, then cellxgene with serve a single dataset located at datapath.
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datapath: null
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obs_names: null
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var_names: null
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about: null
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title: null
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data_locator:
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s3:
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# s3 region name.
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# if true, then the s3 location is automatically determined from the datapath or dataroot.
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# if false/null, then do not set.
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# if a string, then use that value (e.g. us-east-1).
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region_name: true
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adaptor:
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anndata_adaptor:
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backed: false
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limits:
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column_request_max: 32
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diffexp_cellcount_max: null
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dataset:
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app:
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# Scripts can be a list of either file names (string) or dicts containing keys src, integrity and crossorigin.
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# these will be injected into the index template as script tags with these attributes set.
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scripts: []
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# Inline scripts are a list of file names, where the contents of the file will be injected into the index.
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inline_scripts: []
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# allow authentication support
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authentication_enable: true
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presentation:
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max_categories: 1000
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custom_colors: true
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user_annotations:
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enable: true
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type: local_file_csv
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local_file_csv:
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directory: null
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file: null
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ontology:
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enable: false
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obo_location: null
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embeddings:
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names : []
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enable_reembedding: false
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diffexp:
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enable: true
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lfc_cutoff: 0.01
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top_n: 10
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external:
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# You can retrieve configuration parameters from this config file, the environment,
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# the AWS secrets manager, or from the "cellxgene launch" command line arguments.
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# They are applied in that order, meaning that if a parameter is defined in more
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# than one location, the last one applied takes effect.
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# environment variables:
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# This section describes how to map environment variables to configuration parameters.
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# The format is a list defining an environment variable.
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# Each entry in the list is a dictionary with three entries:
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# name: the name of the environment variable
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# path: the path within the cellxgene configuration to update.
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# required: (default=False) a boolean. If true, then it is an error if the environment variable is not set.
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environment:
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- name: CXG_SECRET_KEY
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path: [server, app, flask_secret_key]
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required: false
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# AWS Secrets Manager
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# This section describes how to map aws secrets to configuration parameters.
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# The format is the region for the secrets manager, then a list of secrets.
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# each secret has a name, and a list of values.
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# Each entry in the list of values is a dictionary with three entries:
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# key: the key of the aws secret.
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# path: the path within the cellxgene configuration to update.
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# required: (default=False) a boolean. If true, then it is an error if the key does not exist in the secret.
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#
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# example:
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# aws_secrets_manager:
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# region: us-west-2
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# - name: my_first_secret
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# values:
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# - key: flask_secret_key
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# path: [server, app, flask_secret_key]
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# required: true
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# - key: db_uri
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# path: [dataset, user_annotations, db_uri]
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# required: true
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# - name: my_auth_secret
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# values:
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# - key: client_secret
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# path: [server, authentication, client_secret]
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# required: true
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# - key: client_id
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# path: [server, authentication, client_id]
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# required: true
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aws_secrets_manager:
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region: null
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secrets: []
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"""
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def get_default_config():
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return yaml.load(default_config, Loader=yaml.Loader)
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