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.
268 lines
9.9 KiB
Python
268 lines
9.9 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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server_timing_headers: false
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csp_directives: null
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# By default, cellxgene will serve api requests from the same base url as the webpage.
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# In general api_base_url and web_base_url will not need to be set.
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# There are two reasons to set these parameters:
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# 1. Oauth authentication is used; the oauth server will redirect back to the api_base_url after login,
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# which then redirects back to the web_base_url. If the web_base_url is not set, it will default to
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# the api_base_url. If oauth authentication is used, the api_base_url must be set.
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# For a local test (where the server runs on "http://localhost:<port>"), then the api_base_url may be
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# set to the string "local".
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# 2. The cellxgene deploymnent is in an environment where the webpage and api have
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# different base urls. In this case both api_base_url and web_base_url must be set.
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# It is up to the server admin to ensure that the networking is setup correctly for this environment.
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api_base_url: null
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web_base_url: null
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authentication:
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# The authentication types may be "none", "session", "oauth"
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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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# oauth: oauth2 is used for authentication; parameters are defined in params_oauth.
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type: session
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insecure_test_environment: false
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params_oauth:
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# url to the oauth server
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oauth_api_base_url: null
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# client_id of this app
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client_id: null
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# the client_secret known to the auth server and this app
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client_secret: null
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# jwt_decode_options, to specify non default decode options define
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# jwt_decode_options to be a dictionary with key/values described by
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# the options parameter of the jose.jwt.decode function:
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# (https://python-jose.readthedocs.io/en/latest/jwt/api.html)
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jwt_decode_options: null
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# if true, the jwt containing the id_token is stored in a session cookie
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session_cookie: true
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# if session_cookie is false, then a regular cookie will be used. In that case
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# the cookie will be defined by a dictionary of parameters.
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# The keys of the dictionary match the parameters of the flask set_cookie api
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# (https://flask.palletsprojects.com/en/1.1.x/api/), and with the same meaning.
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# legal keys: key, max_age, expires, path, domain, secure, httponly, and samesite.
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cookie: null
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multi_dataset:
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# If dataroot is set, then cellxgene may serve multiple datasets. This parameter is not
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# compatible with single_dataset/datapath.
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# dataroot may be a string, representing the path to a directory or S3 prefix. In this
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# case the datasets in that location are accessed from <server>/d/<datasetname>.
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# example:
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# dataroot: /path/to/datasets/
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# or
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# dataroot: s3://bucket/prefix/
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#
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# As an alternative, dataroot can be a dictionary, where a dataset key is associated with a base_url
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# and a dataroot.
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# example:
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# dataroot:
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# d1:
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# base_url: set1
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# dataroot: /path/to/set1_datasets/
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# d2:
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# base_url: set2/subdir
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# dataroot: /path/to/set2_datasets/
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#
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# In this case, datasets can be accessed from <server>/set1/<datasetname> or
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# <server>/set2/subdir/<datasetname>. It is possible to have different dataset configurations
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# for datasets accessed through different dataroots. For example, in one dataroot, the
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# user annotations could be enabled, and in another dataroot they could be disabled.
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# To specify dataroot configurations, add a new top level dictionary to the config named
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# per_dataset_config. Within per_dataset_config create a dictionary for each dataroot to specialize
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# ("d1" or "d2" from the example). Each of these dictionaries has the exact same form as the "dataset"
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# dictionary (see below).
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# When this approach is used, the values for each configuration option are checked in
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# this order: per_dataset_config/<key>, dataset, then the default values.
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#
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# example:
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#
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# per_dataset_config:
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# d1:
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# user_annotations:
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# enable: false
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# d2:
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# user_annotations:
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# enable: true
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dataroot: null
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# The index page when in multi-dataset mode:
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# false or null: this returns a 404 code
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# true: loads a test index page, which links to the datasets that are available in the dataroot
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# string/URL: redirect to this URL: flask.redirect(config.multi_dataset__index)
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index: false
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# A list of allowed matrix types. If an empty list, then all matrix types are allowed
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allowed_matrix_types: []
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matrix_cache:
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# The maximum number of datasets that may be opened at one time. The least recently used dataset
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# is evicted from the cache first.
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max_datasets: 5
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# A matrix is automatically removed from the cache after timelimit_s number of seconds.
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# If timelimit_s is set to None, then there is no time limit.
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timelimit_s: 30
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single_dataset:
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# If datapath is set, then cellxgene with serve a single dataset located at datapath. This parameter is not
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# compatible with multi_dataset/dataroot.
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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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diffexp:
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alg_cxg:
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# The number of threads to use is computed from: min(max_workers, cpu_multipler * cpu_count).
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# Where cpu_count is determined at runtime.
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max_workers: 64
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cpu_multiplier: 4
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# The target number of matrix elements that are evaluated
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# together in one thread.
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target_workunit: 16_000_000
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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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cxg_adaptor:
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# The key/values under tiledb_ctx will be used to initialize the tiledb Context.
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# If 'vfs.s3.region' is not set, then it will automatically use the setting from
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# data_locator / s3 / region_name.
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tiledb_ctx:
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sm.tile_cache_size: 8589934592
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sm.num_reader_threads: 32
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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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about_legal_tos: null
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about_legal_privacy: null
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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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hosted_tiledb_array:
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db_uri: null
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hosted_file_directory: null
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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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- name: CXG_OAUTH_CLIENT_SECRET
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path: [server, authentication, params_oauth, client_secret]
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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, hosted_tiledb_array, 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, params_oauth, client_secret]
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# required: true
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# - key: client_id
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# path: [server, authentication, params_oauth, 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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