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https://github.com/chanzuckerberg/cellxgene.git
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Refactor czi_hosted and server into backend directory, pull common code into backend/common, refactor tests (#2102)
* move local_server -> backend/server server-> backend/czi_hosted, pull common code into backend/common update imports, tests and make commands
This commit is contained in:
Madison Dunitz
@@ -1,267 +0,0 @@
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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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