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
2026-10-02 01:58:12 +08:00 · 2021-03-26 00:27:07 -05:00
parent e6e358ddc8
commit 78c9d24ed4
425 changed files with 734 additions and 5317 deletions
@@ -0,0 +1,138 @@
+import yaml
+
+default_config = """
+server:
+  app:
+    verbose: false
+    debug: false
+    host: localhost
+    port : null
+    open_browser: false
+    force_https: false
+    flask_secret_key: null
+
+  authentication:
+    # The authentication types may be "none" or "session"
+    # none:  No authentication support, features like user_annotations must not be enabled.
+    # session:  A session based userid is automatically generated. (no params needed)
+    type: session
+    insecure_test_environment: false
+
+  single_dataset:
+    # If datapath is set, then cellxgene with serve a single dataset located at datapath.
+    datapath: null
+    obs_names: null
+    var_names: null
+    about: null
+    title: null
+
+  data_locator:
+    s3:
+      # s3 region name.
+      #   if true, then the s3 location is automatically determined from the datapath or dataroot.
+      #   if false/null, then do not set.
+      #   if a string, then use that value (e.g. us-east-1).
+      region_name: true
+
+  adaptor:
+    anndata_adaptor:
+      backed: false
+
+  limits:
+    column_request_max: 32
+    diffexp_cellcount_max: null
+
+
+dataset:
+  app:
+    # Scripts can be a list of either file names (string) or dicts containing keys src, integrity and crossorigin.
+    # these will be injected into the index template as script tags with these attributes set.
+    scripts: []
+    # Inline scripts are a list of file names, where the contents of the file will be injected into the index.
+    inline_scripts: []
+
+    # allow authentication support
+    authentication_enable: true
+
+  presentation:
+    max_categories: 1000
+    custom_colors: true
+
+  user_annotations:
+    enable: true
+    type: local_file_csv
+    local_file_csv:
+      directory: null
+      file: null            # annotations file name
+      gene_sets_file: null  # gene sets file name
+    ontology:
+      enable: false
+      obo_location: null
+    gene_sets:
+      readonly: false       # gene sets CRUD enabled/disabled
+
+  embeddings:
+    names : []
+    enable_reembedding: false
+
+  diffexp:
+    enable: true
+    lfc_cutoff: 0.01
+    top_n: 10
+
+external:
+  # You can retrieve configuration parameters from this config file, the environment,
+  # the AWS secrets manager, or from the "cellxgene launch" command line arguments.
+  # They are applied in that order, meaning that if a parameter is defined in more
+  # than one location, the last one applied takes effect.
+
+  # environment variables:
+  # This section describes how to map environment variables to configuration parameters.
+  # The format is a list defining an environment variable.
+  # Each entry in the list is a dictionary with three entries:
+  # name:  the name of the environment variable
+  # path: the path within the cellxgene configuration to update.
+  # required: (default=False) a boolean.  If true, then it is an error if the environment variable is not set.
+
+  environment:
+     - name: CXG_SECRET_KEY
+       path: [server, app, flask_secret_key]
+       required: false
+
+  # AWS Secrets Manager
+  # This section describes how to map aws secrets to configuration parameters.
+  # The format is the region for the secrets manager, then a list of secrets.
+  # each secret has a name, and a list of values.
+  # Each entry in the list of values is a dictionary with three entries:
+  # key:  the key of the aws secret.
+  # path: the path within the cellxgene configuration to update.
+  # required: (default=False) a boolean.  If true, then it is an error if the key does not exist in the secret.
+  #
+  # example:
+  # aws_secrets_manager:
+  #   region: us-west-2
+  #    - name: my_first_secret
+  #      values:
+  #      - key: flask_secret_key
+  #        path: [server, app, flask_secret_key]
+  #        required: true
+  #      - key: db_uri
+  #        path: [dataset, user_annotations, db_uri]
+  #        required: true
+  #    - name:  my_auth_secret
+  #      values:
+  #      - key: client_secret
+  #        path: [server, authentication, client_secret]
+  #        required: true
+  #      - key: client_id
+  #        path: [server, authentication, client_id]
+  #        required: true
+
+  aws_secrets_manager:
+    region: null
+    secrets: []
+"""
+
+
+def get_default_config():
+    return yaml.load(default_config, Loader=yaml.Loader)