mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-17 13:58:00 +08:00
1ea2b7fe80
* 2211 fixes * lint * lint * add missing test and bug found by test * change terminology for count distribution * update scanpy requirement * update scanpy requirement
138 lines
4.1 KiB
Python
138 lines
4.1 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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generate_cache_control_headers: false
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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 # annotations file name
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gene_sets_file: null # gene sets file name
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gene_sets:
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readonly: false # gene sets CRUD enabled/disabled
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embeddings:
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names : []
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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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X_approx_distribution: auto
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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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