refactor config to support different config options for datasets in different dataroots. (#1596)

This will give us the ability to specify different config options for
different dataroots.

the key of the dataroot dictionary is no longer the same as the dataroot_url.
Previously key==dataroot_url, and now those are separated.

Added an "is_multi_dataset" function to simplify logic where it branched on single vs multi.

Simplified the rest.py interface by no longer passing in the user annotations object, since
that can be retrieved from the dataset.

server/app/app.py

@@ -33,7 +33,7 @@ def _cache_control(always, **cache_kwargs):
         @wraps(f)
         def wrapper(*args, **kwargs):
             response = make_response(f(*args, **kwargs))
-            if not always and not current_app.app_config.server__generate_cache_control_headers:
+            if not always and not current_app.app_config.server_config.app__generate_cache_control_headers:
                 return response
             if response.status_code >= 400:
                 return response
@@ -61,25 +61,31 @@ def cache_control_always(**cache_kwargs):
 @webbp.route("/", methods=["GET"])
 @cache_control_always(public=True, max_age=0, no_store=True, no_cache=True, must_revalidate=True)
 def dataset_index(url_dataroot=None, dataset=None):
-    config = current_app.app_config
+    app_config = current_app.app_config
+    server_config = app_config.server_config
     if dataset is None:
-        if config.single_dataset__datapath:
+        if app_config.is_multi_dataset():
-            location = config.single_dataset__datapath
-        else:
             return dataroot_index()
+        else:
+            location = server_config.single_dataset__datapath
     else:
-        dataroot = config.multi_dataset__dataroot.get(url_dataroot)
+        dataroot = None
+        for key, dataroot_dict in server_config.multi_dataset__dataroot.items():
+            if dataroot_dict["base_url"] == url_dataroot:
+                dataroot = dataroot_dict["dataroot"]
+                break
         if dataroot is None:
             abort(HTTPStatus.NOT_FOUND)
         location = path_join(dataroot, dataset)
 
-    scripts = config.server__scripts
+    dataset_config = app_config.get_dataset_config(url_dataroot)
-    inline_scripts = config.server__inline_scripts
+    scripts = dataset_config.app__scripts
+    inline_scripts = dataset_config.app__inline_scripts
 
     try:
         cache_manager = current_app.matrix_data_cache_manager
-        with cache_manager.data_adaptor(location, config) as data_adaptor:
+        with cache_manager.data_adaptor(url_dataroot, location, app_config) as data_adaptor:
-            dataset_title = config.get_title(data_adaptor)
+            dataset_title = app_config.get_title(data_adaptor)
             return render_template(
                 "index.html", datasetTitle=dataset_title, SCRIPTS=scripts, INLINE_SCRIPTS=inline_scripts
             )
@@ -103,11 +109,19 @@ def handle_request_exception(error):
 
 def get_data_adaptor(url_dataroot=None, dataset=None):
     config = current_app.app_config
+    server_config = config.server_config
+    dataset_key = None
 
     if dataset is None:
-        datapath = config.single_dataset__datapath
+        datapath = server_config.single_dataset__datapath
     else:
-        dataroot = config.multi_dataset__dataroot.get(url_dataroot)
+        dataroot = None
+        for key, dataroot_dict in server_config.multi_dataset__dataroot.items():
+            if dataroot_dict["base_url"] == url_dataroot:
+                dataroot = dataroot_dict["dataroot"]
+                dataset_key = key
+                break
+
         if dataroot is None:
             raise DatasetAccessError(f"Invalid dataset {url_dataroot}/{dataset}")
         datapath = path_join(dataroot, dataset)
@@ -121,7 +135,7 @@ def get_data_adaptor(url_dataroot=None, dataset=None):
         return common_rest.abort_and_log(HTTPStatus.BAD_REQUEST, "Invalid dataset NONE", loglevel=logging.INFO)
 
     cache_manager = current_app.matrix_data_cache_manager
-    return cache_manager.data_adaptor(datapath, config)
+    return cache_manager.data_adaptor(dataset_key, datapath, config)
 
 
 def rest_get_data_adaptor(func):
@@ -145,9 +159,12 @@ def dataroot_test_index():
     data += "<body><H1>Welcome to cellxgene</H1>"
 
     config = current_app.app_config
+    server_config = config.server_config
     datasets = []
-    for url_dataroot, dataroot in config.multi_dataset__dataroot.items():
+    for dataroot_dict in server_config.multi_dataset__dataroot.values():
-        locator = DataLocator(dataroot, region_name=config.data_locator__s3__region_name)
+        dataroot = dataroot_dict["dataroot"]
+        url_dataroot = dataroot_dict["base_url"]
+        locator = DataLocator(dataroot, region_name=server_config.data_locator__s3__region_name)
         for fname in locator.ls():
             location = path_join(dataroot, fname)
             try:
@@ -171,12 +188,12 @@ def dataroot_test_index():
 def dataroot_index():
     # Handle the base url for the cellxgene server when running in multi dataset mode
     config = current_app.app_config
-    if not config.multi_dataset__index:
+    if not config.server_config.multi_dataset__index:
         abort(HTTPStatus.NOT_FOUND)
-    elif config.multi_dataset__index is True:
+    elif config.server_config.multi_dataset__index is True:
         return dataroot_test_index()
     else:
-        return redirect(config.multi_dataset__index)
+        return redirect(config.server_config.multi_dataset__index)
 
 
 class DatasetResource(Resource):
@@ -191,33 +208,33 @@ class SchemaAPI(DatasetResource):
     @cache_control(public=True, max_age=ONE_WEEK)
     @rest_get_data_adaptor
     def get(self, data_adaptor):
-        return common_rest.schema_get(data_adaptor, current_app.annotations)
+        return common_rest.schema_get(data_adaptor)
 
 
 class ConfigAPI(DatasetResource):
     @cache_control(public=True, max_age=ONE_WEEK)
     @rest_get_data_adaptor
     def get(self, data_adaptor):
-        return common_rest.config_get(current_app.app_config, data_adaptor, current_app.annotations)
+        return common_rest.config_get(current_app.app_config, data_adaptor)
 
 
 class AnnotationsObsAPI(DatasetResource):
     @cache_control(public=True, max_age=ONE_WEEK)
     @rest_get_data_adaptor
     def get(self, data_adaptor):
-        return common_rest.annotations_obs_get(request, data_adaptor, current_app.annotations)
+        return common_rest.annotations_obs_get(request, data_adaptor)
 
     @cache_control(no_store=True)
     @rest_get_data_adaptor
     def put(self, data_adaptor):
-        return common_rest.annotations_obs_put(request, data_adaptor, current_app.annotations)
+        return common_rest.annotations_obs_put(request, data_adaptor)
 
 
 class AnnotationsVarAPI(DatasetResource):
     @cache_control(public=True, max_age=ONE_WEEK)
     @rest_get_data_adaptor
     def get(self, data_adaptor):
-        return common_rest.annotations_var_get(request, data_adaptor, current_app.annotations)
+        return common_rest.annotations_var_get(request, data_adaptor)
 
 
 class DataVarAPI(DatasetResource):
@@ -290,29 +307,26 @@ class Server:
         self.app = Flask(__name__, static_folder="../common/web/static")
         self._before_adding_routes(self.app, app_config)
         self.app.json_encoder = Float32JSONEncoder
-        if app_config.server__server_timing_headers:
+        server_config = app_config.server_config
+        if server_config.app__server_timing_headers:
             ServerTiming(self.app, force_debug=True)
 
         # enable session data
         self.app.permanent_session_lifetime = datetime.timedelta(days=50 * 365)
 
         # Config
-        secret_key = app_config.server__flask_secret_key
+        secret_key = server_config.app__flask_secret_key
         self.app.config.update(SECRET_KEY=secret_key)
 
         self.app.register_blueprint(webbp)
 
         api_version = "/api/v0.2"
-        if app_config.single_dataset__datapath:
+        if app_config.is_multi_dataset():
-            bp_api = Blueprint("api", __name__, url_prefix=api_version)
-            resources = get_api_resources(bp_api)
-            self.app.register_blueprint(resources.blueprint)
-
-        else:
             # NOTE:  These routes only allow the dataset to be in the directory
             # of the dataroot, and not a subdirectory.  We may want to change
             # the route format at some point
-            for url_dataroot in app_config.multi_dataset__dataroot.keys():
+            for dataroot_dict in server_config.multi_dataset__dataroot.values():
+                url_dataroot = dataroot_dict["base_url"]
                 bp_api = Blueprint(
                     f"api_dataset_{url_dataroot}", __name__, url_prefix=f"/{url_dataroot}/<dataset>" + api_version
                 )
@@ -321,9 +335,13 @@ class Server:
                 self.app.add_url_rule(
                     f"/{url_dataroot}/<dataset>/",
                     f"dataset_index_{url_dataroot}",
-                    lambda dataset: dataset_index(url_dataroot, dataset),
+                    lambda dataset, url_dataroot=url_dataroot: dataset_index(url_dataroot, dataset),
                     methods=["GET"],
                 )
-        self.app.matrix_data_cache_manager = app_config.matrix_data_cache_manager
+        else:
-        self.app.annotations = app_config.user_annotations
+            bp_api = Blueprint("api", __name__, url_prefix=api_version)
+            resources = get_api_resources(bp_api)
+            self.app.register_blueprint(resources.blueprint)
+
+        self.app.matrix_data_cache_manager = server_config.matrix_data_cache_manager
         self.app.app_config = app_config

server/cli/launch.py

@@ -22,13 +22,13 @@ def annotation_args(func):
     @click.option(
         "--disable-annotations",
         is_flag=True,
-        default=not DEFAULT_CONFIG.user_annotations__enable,
+        default=not DEFAULT_CONFIG.default_dataset_config.user_annotations__enable,
         show_default=True,
         help="Disable user annotation of data.",
     )
     @click.option(
         "--annotations-file",
-        default=DEFAULT_CONFIG.user_annotations__local_file_csv__file,
+        default=DEFAULT_CONFIG.default_dataset_config.user_annotations__local_file_csv__file,
         show_default=True,
         multiple=False,
         metavar="<path>",
@@ -37,7 +37,7 @@ def annotation_args(func):
     )
     @click.option(
         "--annotations-dir",
-        default=DEFAULT_CONFIG.user_annotations__local_file_csv__directory,
+        default=DEFAULT_CONFIG.default_dataset_config.user_annotations__local_file_csv__directory,
         show_default=False,
         multiple=False,
         metavar="<directory path>",
@@ -47,13 +47,13 @@ def annotation_args(func):
     @click.option(
         "--experimental-annotations-ontology",
         is_flag=True,
-        default=DEFAULT_CONFIG.user_annotations__ontology__enable,
+        default=DEFAULT_CONFIG.default_dataset_config.user_annotations__ontology__enable,
         show_default=True,
         help="When creating annotations, optionally autocomplete names from ontology terms.",
     )
     @click.option(
         "--experimental-annotations-ontology-obo",
-        default=DEFAULT_CONFIG.user_annotations__ontology__obo_location,
+        default=DEFAULT_CONFIG.default_dataset_config.user_annotations__ontology__obo_location,
         show_default=True,
         metavar="<path or url>",
         help="Location of OBO file defining cell annotation autosuggest terms.",
@@ -68,7 +68,7 @@ def annotation_args(func):
 def config_args(func):
     @click.option(
         "--max-category-items",
-        default=DEFAULT_CONFIG.presentation__max_categories,
+        default=DEFAULT_CONFIG.default_dataset_config.presentation__max_categories,
         metavar="<integer>",
         show_default=True,
         help="Will not display categories with more distinct values than specified.",
@@ -83,7 +83,7 @@ def config_args(func):
     @click.option(
         "--diffexp-lfc-cutoff",
         "-de",
-        default=DEFAULT_CONFIG.diffexp__lfc_cutoff,
+        default=DEFAULT_CONFIG.default_dataset_config.diffexp__lfc_cutoff,
         show_default=True,
         metavar="<float>",
         help="Minimum log fold change threshold for differential expression.",
@@ -91,14 +91,14 @@ def config_args(func):
     @click.option(
         "--disable-diffexp",
         is_flag=True,
-        default=not DEFAULT_CONFIG.diffexp__enable,
+        default=not DEFAULT_CONFIG.default_dataset_config.diffexp__enable,
         show_default=False,
         help="Disable on-demand differential expression.",
     )
     @click.option(
         "--embedding",
         "-e",
-        default=DEFAULT_CONFIG.embeddings__names,
+        default=DEFAULT_CONFIG.default_dataset_config.embeddings__names,
         multiple=True,
         show_default=False,
         metavar="<text>",
@@ -107,7 +107,7 @@ def config_args(func):
     @click.option(
         "--experimental-enable-reembedding",
         is_flag=True,
-        default=DEFAULT_CONFIG.embeddings__enable_reembedding,
+        default=DEFAULT_CONFIG.default_dataset_config.embeddings__enable_reembedding,
         show_default=False,
         hidden=True,
         help="Enable experimental on-demand re-embedding using UMAP. WARNING: may be very slow.",
@@ -123,14 +123,14 @@ def dataset_args(func):
     @click.option(
         "--obs-names",
         "-obs",
-        default=DEFAULT_CONFIG.single_dataset__obs_names,
+        default=DEFAULT_CONFIG.server_config.single_dataset__obs_names,
         metavar="<text>",
         help="Name of annotation field to use for observations. If not specified cellxgene will use the the obs index.",
     )
     @click.option(
         "--var-names",
         "-var",
-        default=DEFAULT_CONFIG.single_dataset__var_names,
+        default=DEFAULT_CONFIG.server_config.single_dataset__var_names,
         metavar="<text>",
         help="Name of annotation to use for variables. If not specified cellxgene will use the the var index.",
     )
@@ -138,20 +138,20 @@ def dataset_args(func):
         "--backed",
         "-b",
         is_flag=True,
-        default=DEFAULT_CONFIG.adaptor__anndata_adaptor__backed,
+        default=DEFAULT_CONFIG.server_config.adaptor__anndata_adaptor__backed,
         show_default=False,
         help="Load anndata in file-backed mode. " "This may save memory, but may result in slower overall performance.",
     )
     @click.option(
         "--title",
         "-t",
-        default=DEFAULT_CONFIG.single_dataset__title,
+        default=DEFAULT_CONFIG.server_config.single_dataset__title,
         metavar="<text>",
         help="Title to display. If omitted will use file name.",
     )
     @click.option(
         "--about",
-        default=DEFAULT_CONFIG.single_dataset__about,
+        default=DEFAULT_CONFIG.server_config.single_dataset__about,
         metavar="<URL>",
         help="URL providing more information about the dataset (hint: must be a fully specified absolute URL).",
     )
@@ -167,7 +167,7 @@ def server_args(func):
         "--debug",
         "-d",
         is_flag=True,
-        default=DEFAULT_CONFIG.server__debug,
+        default=DEFAULT_CONFIG.server_config.app__debug,
         show_default=True,
         help="Run in debug mode. This is helpful for cellxgene developers, "
         "or when you want more information about an error condition.",
@@ -176,7 +176,7 @@ def server_args(func):
         "--verbose",
         "-v",
         is_flag=True,
-        default=DEFAULT_CONFIG.server__verbose,
+        default=DEFAULT_CONFIG.server_config.app__verbose,
         show_default=True,
         help="Provide verbose output, including warnings and all server requests.",
     )
@@ -184,7 +184,7 @@ def server_args(func):
         "--port",
         "-p",
         metavar="<port>",
-        default=DEFAULT_CONFIG.server__port,
+        default=DEFAULT_CONFIG.server_config.app__port,
         type=int,
         show_default=True,
         help="Port to run server on. If not specified cellxgene will find an available port.",
@@ -192,14 +192,14 @@ def server_args(func):
     @click.option(
         "--host",
         metavar="<IP address>",
-        default=DEFAULT_CONFIG.server__host,
+        default=DEFAULT_CONFIG.server_config.app__host,
         show_default=False,
         help="Host IP address. By default cellxgene will use localhost (e.g. 127.0.0.1).",
     )
     @click.option(
         "--scripts",
         "-s",
-        default=DEFAULT_CONFIG.server__scripts,
+        default=DEFAULT_CONFIG.default_dataset_config.app__scripts,
         multiple=True,
         metavar="<text>",
         help="Additional script files to include in HTML page. If not specified, "
@@ -220,7 +220,7 @@ def launch_args(func):
     @server_args
     @click.option(
         "--dataroot",
-        default=DEFAULT_CONFIG.multi_dataset__dataroot,
+        default=DEFAULT_CONFIG.server_config.multi_dataset__dataroot,
         metavar="<data directory>",
         help="Enable cellxgene to serve multiple files. Supply path (local directory or URL)"
         " to folder containing H5AD and/or CXG datasets.",
@@ -232,7 +232,7 @@ def launch_args(func):
         "-o",
         "open_browser",
         is_flag=True,
-        default=DEFAULT_CONFIG.server__open_browser,
+        default=DEFAULT_CONFIG.server_config.app__open_browser,
         show_default=True,
         help="Open web browser after launch.",
     )
@@ -296,7 +296,7 @@ class CliLaunchServer(Server):
             "application/octet-stream",
         ]
         Compress(app)
-        if app_config.server__debug:
+        if app_config.server_config.app__debug:
             CORS(app, supports_credentials=True)
 
 
@@ -362,6 +362,7 @@ def launch(
 
     # app config
     app_config = AppConfig()
+    server_config = app_config.server_config
 
     try:
         if config_file:
@@ -370,19 +371,22 @@ def launch(
         # Determine which config options were give on the command line.
         # Those will override the ones provided in the config file (if provided).
         cli_config = AppConfig()
-        cli_config.update(
+        cli_config.update_server_config(
-            server__verbose=verbose,
+            app__verbose=verbose,
-            server__debug=debug,
+            app__debug=debug,
-            server__host=host,
+            app__host=host,
-            server__port=port,
+            app__port=port,
-            server__scripts=scripts,
+            app__open_browser=open_browser,
-            server__open_browser=open_browser,
             single_dataset__datapath=datapath,
             single_dataset__title=title,
             single_dataset__about=about,
             single_dataset__obs_names=obs_names,
             single_dataset__var_names=var_names,
             multi_dataset__dataroot=dataroot,
+            adaptor__anndata_adaptor__backed=backed,
+        )
+        cli_config.update_default_dataset_config(
+            app__scripts=scripts,
             user_annotations__enable=not disable_annotations,
             user_annotations__local_file_csv__file=annotations_file,
             user_annotations__local_file_csv__directory=annotations_dir,
@@ -394,13 +398,15 @@ def launch(
             embeddings__enable_reembedding=experimental_enable_reembedding,
             diffexp__enable=not disable_diffexp,
             diffexp__lfc_cutoff=diffexp_lfc_cutoff,
-            adaptor__anndata_adaptor__backed=backed,
         )
-        diff = cli_config.changes_from_default()
+
-        changes = {}
+        diff = cli_config.server_config.changes_from_default()
-        for key, val, defval in diff:
+        changes = {key: val for key, val, _ in diff}
-            changes[key] = val
+        app_config.update_server_config(**changes)
-        app_config.update(**changes)
+
+        diff = cli_config.default_dataset_config.changes_from_default()
+        changes = {key: val for key, val, _ in diff}
+        app_config.update_default_dataset_config(**changes)
 
         # process the configuration
         #  any errors will be thrown as an exception.
@@ -410,8 +416,8 @@ def launch(
             click.echo("[cellxgene] " + message)
 
         # Use a default secret if one is not provided
-        if not app_config.server__flask_secret_key:
+        if not server_config.app__flask_secret_key:
-            app_config.update(server__flask_secret_key="SparkleAndShine")
+            app_config.update_server_config(app__flask_secret_key="SparkleAndShine")
 
         app_config.complete_config(messagefn)
 
@@ -423,12 +429,12 @@ def launch(
     # create the server
     server = CliLaunchServer(app_config)
 
-    if not app_config.server__verbose:
+    if not server_config.app__verbose:
         log = logging.getLogger("werkzeug")
         log.setLevel(logging.ERROR)
 
-    cellxgene_url = f"http://{app_config.server__host}:{app_config.server__port}"
+    cellxgene_url = f"http://{app_config.server_config.app__host}:{app_config.server_config.app__port}"
-    if app_config.server__open_browser:
+    if server_config.app__open_browser:
         click.echo(f"[cellxgene] Launching! Opening your browser to {cellxgene_url} now.")
         webbrowser.open(cellxgene_url)
     else:
@@ -436,16 +442,16 @@ def launch(
 
     click.echo("[cellxgene] Type CTRL-C at any time to exit.")
 
-    if not app_config.server__verbose:
+    if not server_config.app__verbose:
         f = open(devnull, "w")
         sys.stdout = f
 
     try:
         server.app.run(
-            host=app_config.server__host,
+            host=server_config.app__host,
-            debug=app_config.server__debug,
+            debug=server_config.app__debug,
-            port=app_config.server__port,
+            port=server_config.app__port,
-            threaded=not app_config.server__debug,
+            threaded=not server_config.app__debug,
             use_debugger=False,
             use_reloader=False,
         )

server/common/app_config.py

@@ -38,170 +38,110 @@ class AppFeature(object):
 
 
 class AppConfig(object):
+    """AppConfig stores all the configuration for cellxgene.  The configuration is divided into two main parts:
+    server attributes, and dataset attributes. The server_config contains attributes that refer to the server process
+    as a whole.   The default_dataset_config referes to attributes that are associated with the features and
+    presentations of a dataset.  The dataset config attributes can be overridden depending on the url by which the
+    dataset was accessed.  These are stored in dataroot_config.
+    AppConfig has methods to initialize, modify, and access the configuration.
+    """
+
     def __init__(self):
 
+        # the default configuration (see default_config.py)
         self.default_config = get_default_config()
-        self.attr_checked = {k: False for k in self.__mapping(self.default_config).keys()}
+        # the server configuration
-
+        self.server_config = ServerConfig(self, self.default_config["server"])
-        dc = self.default_config
+        # the dataset config, unless overridden by an entry in dataroot_config
-        try:
+        self.default_dataset_config = DatasetConfig(None, self, self.default_config["dataset"])
-            self.server__verbose = dc["server"]["verbose"]
+        # a dictionary of keys to DatasetConfig objects.  Each key must exist in the multi_dataset__dataroot
-            self.server__debug = dc["server"]["debug"]
+        # attribute of the server_config.
-            self.server__host = dc["server"]["host"]
+        self.dataroot_config = {}
-            self.server__port = dc["server"]["port"]
-            self.server__scripts = dc["server"]["scripts"]
-            self.server__inline_scripts = dc["server"]["inline_scripts"]
-            self.server__open_browser = dc["server"]["open_browser"]
-            self.server__about_legal_tos = dc["server"]["about_legal_tos"]
-            self.server__about_legal_privacy = dc["server"]["about_legal_privacy"]
-            self.server__force_https = dc["server"]["force_https"]
-            self.server__flask_secret_key = dc["server"]["flask_secret_key"]
-            self.server__generate_cache_control_headers = dc["server"]["generate_cache_control_headers"]
-            self.server__server_timing_headers = dc["server"]["server_timing_headers"]
-            self.server__csp_directives = dc["server"]["csp_directives"]
-
-            self.multi_dataset__dataroot = dc["multi_dataset"]["dataroot"]
-            self.multi_dataset__index = dc["multi_dataset"]["index"]
-            self.multi_dataset__allowed_matrix_types = dc["multi_dataset"]["allowed_matrix_types"]
-            self.multi_dataset__matrix_cache__max_datasets = dc["multi_dataset"]["matrix_cache"]["max_datasets"]
-            self.multi_dataset__matrix_cache__timelimit_s = dc["multi_dataset"]["matrix_cache"]["timelimit_s"]
-
-            self.single_dataset__datapath = dc["single_dataset"]["datapath"]
-            self.single_dataset__obs_names = dc["single_dataset"]["obs_names"]
-            self.single_dataset__var_names = dc["single_dataset"]["var_names"]
-            self.single_dataset__about = dc["single_dataset"]["about"]
-            self.single_dataset__title = dc["single_dataset"]["title"]
-
-            self.user_annotations__enable = dc["user_annotations"]["enable"]
-            self.user_annotations__type = dc["user_annotations"]["type"]
-            self.user_annotations__local_file_csv__directory = dc["user_annotations"]["local_file_csv"]["directory"]
-            self.user_annotations__local_file_csv__file = dc["user_annotations"]["local_file_csv"]["file"]
-            self.user_annotations__ontology__enable = dc["user_annotations"]["ontology"]["enable"]
-            self.user_annotations__ontology__obo_location = dc["user_annotations"]["ontology"]["obo_location"]
-
-            self.presentation__max_categories = dc["presentation"]["max_categories"]
-            self.presentation__custom_colors = dc["presentation"]["custom_colors"]
-
-            self.embeddings__names = dc["embeddings"]["names"]
-            self.embeddings__enable_reembedding = dc["embeddings"]["enable_reembedding"]
-
-            self.diffexp__enable = dc["diffexp"]["enable"]
-            self.diffexp__lfc_cutoff = dc["diffexp"]["lfc_cutoff"]
-            self.diffexp__top_n = dc["diffexp"]["top_n"]
-            self.diffexp__alg_cxg__max_workers = dc["diffexp"]["alg_cxg"]["max_workers"]
-            self.diffexp__alg_cxg__cpu_multiplier = dc["diffexp"]["alg_cxg"]["cpu_multiplier"]
-            self.diffexp__alg_cxg__target_workunit = dc["diffexp"]["alg_cxg"]["target_workunit"]
-
-            self.data_locator__s3__region_name = dc["data_locator"]["s3"]["region_name"]
-
-            self.adaptor__cxg_adaptor__tiledb_ctx = dc["adaptor"]["cxg_adaptor"]["tiledb_ctx"]
-            self.adaptor__anndata_adaptor__backed = dc["adaptor"]["anndata_adaptor"]["backed"]
-
-            self.limits__diffexp_cellcount_max = dc["limits"]["diffexp_cellcount_max"]
-            self.limits__column_request_max = dc["limits"]["column_request_max"]
-
-        except KeyError as e:
-            raise ConfigurationError(f"Unexpected config: {str(e)}")
-
-        # The annotation object is created during complete_config and stored here.
-        self.user_annotations = None
-
-        # The matrix data cache manager is created during the complete_config and stored here.
-        self.matrix_data_cache_manager = None
 
         # Set to true when config_completed is called
         self.is_completed = False
 
+    def get_dataset_config(self, dataroot_key):
+        if self.server_config.single_dataset__datapath:
+            return self.default_dataset_config
+        else:
+            return self.dataroot_config.get(dataroot_key, self.default_dataset_config)
+
     def check_config(self):
+        """Verify all the attributes have been checked"""
         if not self.is_completed:
             raise ConfigurationError("The configuration has not been completed")
-        mapping = self.__mapping(self.default_config)
+        self.server_config.check_config()
-        for key in mapping.keys():
+        self.default_dataset_config.check_config()
-            if not self.attr_checked[key]:
+        for dataset_config in self.dataroot_config.values():
-                raise ConfigurationError(f"The attr '{key}' has not been checked")
+            dataset_config.check_config()
 
-    def __mapping(self, config):
+    def update_server_config(self, **kw):
-        """Create a mapping from attribute names to (location in the config tree, value)"""
+        self.server_config.update(**kw)
-        dc = copy.deepcopy(config)
+        self.is_complete = False
-        mapping = {}
 
-        # special cases where the value could be a dict.
+    def update_default_dataset_config(self, **kw):
-        # If its value is not None, the entry is added to the mapping, and not included
+        self.default_dataset_config.update(**kw)
-        # in the flattening below.
+        # update all the other dataset configs, if any
-        dictval_cases = [
+        for value in self.dataroot_config.values():
-            ("adaptor", "cxg_adaptor", "tiledb_ctx"),
+            value.update(**kw)
-            ("server", "csp_directives"),
+        self.is_complete = False
-            ("multi_dataset", "dataroot"),
-        ]
-        for dictval_case in dictval_cases:
-            cur = dc
-            for part in dictval_case[:-1]:
-                cur = cur.get(part, {})
-            val = cur.get(dictval_case[-1])
-            if val is not None:
-                key = "__".join(dictval_case)
-                mapping[key] = (dictval_case, val)
-                del cur[dictval_case[-1]]
-
-        flat_config = flatten(dc)
-        for key, value in flat_config.items():
-            # name of the attribute
-            attr = "__".join(key)
-            mapping[attr] = (key, value)
-
-        return mapping
 
     def update_from_config_file(self, config_file):
         with open(config_file) as fyaml:
             config = yaml.load(fyaml, Loader=yaml.FullLoader)
 
-        mapping = self.__mapping(config)
+        self.server_config.update_from_config(config["server"], "server")
-        for attr, (key, value) in mapping.items():
+        self.default_dataset_config.update_from_config(config["dataset"], "dataset")
-            if not hasattr(self, attr):
-                raise ConfigurationError(f"Unknown key from config file: {key}")
-            try:
-                setattr(self, attr, value)
-            except KeyError:
-                raise ConfigurationError(f"Unable to set config attribute: {key}")
 
-            self.attr_checked[attr] = False
+        per_dataset_config = config.get("per_dataset_config", {})
+        for key, dataroot_config in per_dataset_config.items():
+            self.add_dataroot_config(key, **dataroot_config)
 
-        self.is_completed = False
+        self.is_complete = False
 
     def write_config(self, config_file):
         """output the config to a yaml file"""
-        mapping = self.__mapping(self.default_config)
+        server = self.server_config.create_mapping(self.server_config.default_config)
-        for attrname in mapping.keys():
+        dataset = self.default_dataset_config.create_mapping(self.default_dataset_config.default_config)
-            mapping[attrname] = getattr(self, attrname)
+        config = dict(server={}, dataset={})
-        config = unflatten(mapping, splitter=lambda key: key.split("__"))
+        for attrname in server.keys():
+            config["server__" + attrname] = getattr(self.server_config, attrname)
+        for attrname in dataset.keys():
+            config["dataset__" + attrname] = getattr(self.default_dataset_config, attrname)
+        if self.dataroot_config:
+            config["per_dataset_config"] = {}
+        for dataroot_tag, dataroot_config in self.dataroot_config.items():
+            dataset = dataroot_config.create_mapping(dataroot_config.default_config)
+            for attrname in dataset.keys():
+                config[f"per_dataset_config__{dataroot_tag}__" + attrname] = getattr(dataroot_config, attrname)
+
+        config = unflatten(config, splitter=lambda key: key.split("__"))
         yaml.dump(config, open(config_file, "w"))
 
-    def update(self, **kw):
-        for key, value in kw.items():
-            if not hasattr(self, key):
-                raise ConfigurationError(f"unknown config parameter {key}.")
-            try:
-                if type(value) == tuple:
-                    # convert tuple values to list values
-                    value = list(value)
-                setattr(self, key, value)
-            except KeyError:
-                raise ConfigurationError(f"Unable to set config parameter {key}.")
-
-            self.attr_checked[key] = False
-
-        self.is_completed = False
-
     def changes_from_default(self):
         """Return all the attribute that are different from the default"""
-        mapping = self.__mapping(self.default_config)
+        diff_server = self.server_config.changes_from_default()
-        diff = []
+        diff_dataset = self.default_dataset_config.changes_from_default()
-        for attrname, (key, defval) in mapping.items():
+        diff = dict(server=diff_server, dataset=diff_dataset)
-            curval = getattr(self, attrname)
-            if curval != defval:
-                diff.append((attrname, curval, defval))
         return diff
 
+    def add_dataroot_config(self, dataroot_tag, **kw):
+        """Create a new dataset config object based on the default dataset config, and kw parameters"""
+        if dataroot_tag in self.dataroot_config:
+            raise ConfigurationError(f"dataroot config already exists: {dataroot_tag}")
+        if type(self.server_config.multi_dataset__dataroot) != dict:
+            raise ConfigurationError("The server__multi_dataset__dataroot must be a dictionary")
+        if dataroot_tag not in self.server_config.multi_dataset__dataroot:
+            raise ConfigurationError(f"The dataroot_tag ({dataroot_tag}) not found in server__multi_dataset__dataroot")
+
+        self.is_completed = False
+        self.dataroot_config[dataroot_tag] = DatasetConfig(dataroot_tag, self, self.default_config["dataset"])
+        flat_config = self.default_dataset_config.create_mapping(self.default_dataset_config.default_config)
+        config = {key: value[1] for key, value in flat_config.items()}
+        self.dataroot_config[dataroot_tag].update(**config)
+        self.dataroot_config[dataroot_tag].update_from_config(kw, dataroot_tag)
+
     def complete_config(self, messagefn=None):
         """The configure options are checked, and any additional setup based on the config
         parameters is done"""
@@ -218,22 +158,149 @@ class AppConfig(object):
         # messages we can give correct context for attributes with bad value.
         context = dict(messagefn=messagefn)
 
-        self.handle_server(context)
+        self.server_config.complete_config(context)
-        self.handle_adaptor(context)
+        self.default_dataset_config.complete_config(context)
-        self.handle_data_locator(context)
+        for dataroot_config in self.dataroot_config.values():
-        self.handle_adaptor(context)  # may depend on data_locator
+            dataroot_config.complete_config(context)
-        self.handle_presentation(context)
-        self.handle_single_dataset(context)  # may depend on adaptor
-        self.handle_multi_dataset(context)  # may depend on adaptor
-        self.handle_user_annotations(context)
-        self.handle_embeddings(context)
-        self.handle_diffexp(context)
-        self.handle_limits(context)
 
         self.is_completed = True
         self.check_config()
 
-    def __check_attr(self, attrname, vtype):
+    def get_matrix_data_cache_manager(self):
+        return self.server_config.matrix_data_cache_manager
+
+    def is_multi_dataset(self):
+        return self.server_config.multi_dataset__dataroot is not None
+
+    def get_title(self, data_adaptor):
+        return (
+            self.server_config.single_dataset__title
+            if self.server_config.single_dataset__title
+            else data_adaptor.get_title()
+        )
+
+    def get_about(self, data_adaptor):
+        return (
+            self.server_config.single_dataset__about
+            if self.server_config.single_dataset__about
+            else data_adaptor.get_about()
+        )
+
+    def get_client_config(self, data_adaptor):
+        """
+        Return the configuration as required by the /config REST route
+        """
+
+        server_config = self.server_config
+        dataset_config = data_adaptor.dataset_config
+        annotation = dataset_config.user_annotations
+
+        # FIXME The current set of config is not consistently presented:
+        # we have camalCase, hyphen-text, and underscore_text
+
+        # make sure the configuration has been checked.
+        self.check_config()
+
+        # features
+        features = [f.todict() for f in data_adaptor.get_features(annotation)]
+
+        # display_names
+        title = self.get_title(data_adaptor)
+        about = self.get_about(data_adaptor)
+
+        display_names = dict(engine=data_adaptor.get_name(), dataset=title)
+
+        # library_versions
+        library_versions = {}
+        library_versions.update(data_adaptor.get_library_versions())
+        library_versions["cellxgene"] = cellxgene_version
+
+        # links
+        links = {"about-dataset": about}
+
+        # parameters
+        parameters = {
+            "layout": dataset_config.embeddings__names,
+            "max-category-items": dataset_config.presentation__max_categories,
+            "obs_names": server_config.single_dataset__obs_names,
+            "var_names": server_config.single_dataset__var_names,
+            "diffexp_lfc_cutoff": dataset_config.diffexp__lfc_cutoff,
+            "backed": server_config.adaptor__anndata_adaptor__backed,
+            "disable-diffexp": not dataset_config.diffexp__enable,
+            "enable-reembedding": dataset_config.embeddings__enable_reembedding,
+            "annotations": False,
+            "annotations_file": None,
+            "annotations_dir": None,
+            "annotations_cell_ontology_enabled": False,
+            "annotations_cell_ontology_obopath": None,
+            "annotations_cell_ontology_terms": None,
+            "custom_colors": dataset_config.presentation__custom_colors,
+            "diffexp-may-be-slow": False,
+            "about_legal_tos": dataset_config.app__about_legal_tos,
+            "about_legal_privacy": dataset_config.app__about_legal_privacy,
+        }
+
+        data_adaptor.update_parameters(parameters)
+        if annotation:
+            annotation.update_parameters(parameters, data_adaptor)
+
+        # gather it all together
+        c = {}
+        config = c["config"] = {}
+        config["features"] = features
+        config["displayNames"] = display_names
+        config["library_versions"] = library_versions
+        config["links"] = links
+        config["parameters"] = parameters
+        config["limits"] = {
+            "column_request_max": server_config.limits__column_request_max,
+            "diffexp_cellcount_max": server_config.limits__diffexp_cellcount_max,
+        }
+
+        return c
+
+
+class BaseConfig(object):
+    """This class handles the mechanics of updating and checking attributes.
+    Derived classes are expected to store the actual attributes"""
+
+    def __init__(self, app_config, default_config, dictval_cases={}):
+        # reference back to the app_config
+        self.app_config = app_config
+        # the complete set of attribute and their default values (unflattened)
+        self.default_config = default_config
+        # attributes where the value may be a dict (and therefore are not flattened)
+        self.dictval_cases = dictval_cases
+        # used to make sure every attribute value is checked
+        self.attr_checked = {k: False for k in self.create_mapping(default_config).keys()}
+
+    def create_mapping(self, config):
+        """Create a mapping from attribute names to (location in the config tree, value)"""
+        dc = copy.deepcopy(config)
+        mapping = {}
+
+        # special cases where the value could be a dict.
+        # If its value is not None, the entry is added to the mapping, and not included
+        # in the flattening below.
+        for dictval_case in self.dictval_cases:
+            cur = dc
+            for part in dictval_case[:-1]:
+                cur = cur.get(part, {})
+            val = cur.get(dictval_case[-1])
+            if val is not None:
+                key = "__".join(dictval_case)
+                mapping[key] = (dictval_case, val)
+                del cur[dictval_case[-1]]
+
+        flat_config = flatten(dc)
+        for key, value in flat_config.items():
+            # name of the attribute
+            attr = "__".join(key)
+            mapping[attr] = (key, value)
+
+        return mapping
+
+    def check_attr(self, attrname, vtype):
         val = getattr(self, attrname)
         if type(vtype) in (list, tuple):
             if type(val) not in vtype:
@@ -250,48 +317,152 @@ class AppConfig(object):
 
         self.attr_checked[attrname] = True
 
-    def handle_server(self, context):
+    def check_config(self):
-        self.__check_attr("server__verbose", bool)
+        mapping = self.create_mapping(self.default_config)
-        self.__check_attr("server__debug", bool)
+        for key in mapping.keys():
-        self.__check_attr("server__host", str)
+            if not self.attr_checked[key]:
-        self.__check_attr("server__port", (type(None), int))
+                raise ConfigurationError(f"The attr '{key}' has not been checked")
-        self.__check_attr("server__scripts", list)
-        self.__check_attr("server__inline_scripts", list)
-        self.__check_attr("server__open_browser", bool)
-        self.__check_attr("server__force_https", bool)
-        self.__check_attr("server__flask_secret_key", (type(None), str))
-        self.__check_attr("server__generate_cache_control_headers", bool)
-        self.__check_attr("server__about_legal_tos", (type(None), str))
-        self.__check_attr("server__about_legal_privacy", (type(None), str))
-        self.__check_attr("server__server_timing_headers", bool)
-        self.__check_attr("server__csp_directives", (type(None), dict))
 
-        if self.server__port:
+    def update(self, **kw):
-            if not is_port_available(self.server__host, self.server__port):
+        for key, value in kw.items():
+            if not hasattr(self, key):
+                raise ConfigurationError(f"unknown config parameter {key}.")
+            try:
+                if type(value) == tuple:
+                    # convert tuple values to list values
+                    value = list(value)
+                setattr(self, key, value)
+            except KeyError:
+                raise ConfigurationError(f"Unable to set config parameter {key}.")
+
+            self.attr_checked[key] = False
+
+    def update_from_config(self, config, prefix):
+        mapping = self.create_mapping(config)
+        for attr, (key, value) in mapping.items():
+            if not hasattr(self, attr):
+                raise ConfigurationError(f"Unknown key from config file: {prefix}__{attr}")
+            try:
+                setattr(self, attr, value)
+            except KeyError:
+                raise ConfigurationError(f"Unable to set config attribute: {prefix}__{attr}")
+
+            self.attr_checked[attr] = False
+
+    def changes_from_default(self):
+        """Return all the attribute that are different from the default"""
+        mapping = self.create_mapping(self.default_config)
+        diff = []
+        for attrname, (key, defval) in mapping.items():
+            curval = getattr(self, attrname)
+            if curval != defval:
+                diff.append((attrname, curval, defval))
+        return diff
+
+
+class ServerConfig(BaseConfig):
+    """Manages the config attribute associated with the server."""
+
+    def __init__(self, app_config, default_config):
+        dictval_cases = [
+            ("app", "csp_directives"),
+            ("adaptor", "cxg_adaptor", "tiledb_ctx"),
+            ("multi_dataset", "dataroot"),
+        ]
+        super().__init__(app_config, default_config, dictval_cases)
+
+        dc = default_config
+        try:
+            self.app__verbose = dc["app"]["verbose"]
+            self.app__debug = dc["app"]["debug"]
+            self.app__host = dc["app"]["host"]
+            self.app__port = dc["app"]["port"]
+            self.app__open_browser = dc["app"]["open_browser"]
+            self.app__force_https = dc["app"]["force_https"]
+            self.app__flask_secret_key = dc["app"]["flask_secret_key"]
+            self.app__generate_cache_control_headers = dc["app"]["generate_cache_control_headers"]
+            self.app__server_timing_headers = dc["app"]["server_timing_headers"]
+            self.app__csp_directives = dc["app"]["csp_directives"]
+
+            self.multi_dataset__dataroot = dc["multi_dataset"]["dataroot"]
+            self.multi_dataset__index = dc["multi_dataset"]["index"]
+            self.multi_dataset__allowed_matrix_types = dc["multi_dataset"]["allowed_matrix_types"]
+            self.multi_dataset__matrix_cache__max_datasets = dc["multi_dataset"]["matrix_cache"]["max_datasets"]
+            self.multi_dataset__matrix_cache__timelimit_s = dc["multi_dataset"]["matrix_cache"]["timelimit_s"]
+
+            self.single_dataset__datapath = dc["single_dataset"]["datapath"]
+            self.single_dataset__obs_names = dc["single_dataset"]["obs_names"]
+            self.single_dataset__var_names = dc["single_dataset"]["var_names"]
+            self.single_dataset__about = dc["single_dataset"]["about"]
+            self.single_dataset__title = dc["single_dataset"]["title"]
+
+            self.diffexp__alg_cxg__max_workers = dc["diffexp"]["alg_cxg"]["max_workers"]
+            self.diffexp__alg_cxg__cpu_multiplier = dc["diffexp"]["alg_cxg"]["cpu_multiplier"]
+            self.diffexp__alg_cxg__target_workunit = dc["diffexp"]["alg_cxg"]["target_workunit"]
+
+            self.data_locator__s3__region_name = dc["data_locator"]["s3"]["region_name"]
+
+            self.adaptor__cxg_adaptor__tiledb_ctx = dc["adaptor"]["cxg_adaptor"]["tiledb_ctx"]
+            self.adaptor__anndata_adaptor__backed = dc["adaptor"]["anndata_adaptor"]["backed"]
+
+            self.limits__diffexp_cellcount_max = dc["limits"]["diffexp_cellcount_max"]
+            self.limits__column_request_max = dc["limits"]["column_request_max"]
+
+        except KeyError as e:
+            raise ConfigurationError(f"Unexpected config: {str(e)}")
+
+        # The matrix data cache manager is created during the complete_config and stored here.
+        self.matrix_data_cache_manager = None
+
+    def complete_config(self, context):
+        self.handle_app(context)
+        self.handle_data_locator(context)
+        self.handle_adaptor(context)  # may depend on data_locator
+        self.handle_single_dataset(context)  # may depend on adaptor
+        self.handle_multi_dataset(context)  # may depend on adaptor
+        self.handle_diffexp(context)
+        self.handle_limits(context)
+
+        self.check_config()
+
+    def handle_app(self, context):
+        self.check_attr("app__verbose", bool)
+        self.check_attr("app__debug", bool)
+        self.check_attr("app__host", str)
+        self.check_attr("app__port", (type(None), int))
+        self.check_attr("app__open_browser", bool)
+        self.check_attr("app__force_https", bool)
+        self.check_attr("app__flask_secret_key", (type(None), str))
+        self.check_attr("app__generate_cache_control_headers", bool)
+        self.check_attr("app__server_timing_headers", bool)
+        self.check_attr("app__csp_directives", (type(None), dict))
+
+        if self.app__port:
+            if not is_port_available(self.app__host, self.app__port):
                 raise ConfigurationError(
-                    f"The port selected {self.server__port} is in use, please configure an open port."
+                    f"The port selected {self.app__port} is in use, please configure an open port."
                 )
         else:
-            self.server__port = find_available_port(self.server__host, DEFAULT_SERVER_PORT)
+            self.app__port = find_available_port(self.app__host, DEFAULT_SERVER_PORT)
 
-        if self.server__debug:
+        if self.app__debug:
             context["messagefn"]("in debug mode, setting verbose=True and open_browser=False")
-            self.server__verbose = True
+            self.app__verbose = True
-            self.server__open_browser = False
+            self.app__open_browser = False
         else:
             warnings.formatwarning = custom_format_warning
 
-        if not self.server__verbose:
+        if not self.app__verbose:
             sys.tracebacklimit = 0
 
         # secret key:
         #   first, from CXG_SECRET_KEY environment variable
         #   second, from config file
-        self.server__flask_secret_key = os.environ.get("CXG_SECRET_KEY", self.server__flask_secret_key)
+        self.app__flask_secret_key = os.environ.get("CXG_SECRET_KEY", self.app__flask_secret_key)
 
         # CSP Directives are a dict of string: list(string) or string: string
-        if self.server__csp_directives is not None:
+        if self.app__csp_directives is not None:
-            for k, v in self.server__csp_directives.items():
+            for k, v in self.app__csp_directives.items():
                 if not isinstance(k, str):
                     raise ConfigurationError("CSP directive names must be a string.")
                 if isinstance(v, list):
@@ -301,26 +472,15 @@ class AppConfig(object):
                 elif not isinstance(v, str):
                     raise ConfigurationError("CSP directive value must be a string or list of strings.")
 
-        # scripts can be string (filename) or dict (attributes).   Convert string to dict.
-        scripts = []
-        for s in self.server__scripts:
-            if isinstance(s, str):
-                scripts.append({"src": s})
-            elif isinstance(s, dict) and isinstance(s["src"], str):
-                scripts.append(s)
-            else:
-                raise ConfigurationError("Scripts must be string or dict")
-        self.server__scripts = scripts
-
     def handle_data_locator(self, context):
-        self.__check_attr("data_locator__s3__region_name", (type(None), bool, str))
+        self.check_attr("data_locator__s3__region_name", (type(None), bool, str))
         if self.data_locator__s3__region_name is True:
             path = self.single_dataset__datapath or self.multi_dataset__dataroot
             if type(path) == dict:
                 # if multi_dataset__dataroot is a dict, then use the first key
                 # that is in s3.   NOTE:  it is not supported to have dataroots
                 # in different regions.
-                paths = path.values()
+                paths = [val.get("dataroot") for val in path.values()]
                 for path in paths:
                     if path.startswith("s3://"):
                         break
@@ -332,16 +492,12 @@ class AppConfig(object):
                 region_name = None
             self.data_locator__s3__region_name = region_name
 
-    def handle_presentation(self, context):
-        self.__check_attr("presentation__max_categories", int)
-        self.__check_attr("presentation__custom_colors", bool)
-
     def handle_single_dataset(self, context):
-        self.__check_attr("single_dataset__datapath", (str, type(None)))
+        self.check_attr("single_dataset__datapath", (str, type(None)))
-        self.__check_attr("single_dataset__title", (str, type(None)))
+        self.check_attr("single_dataset__title", (str, type(None)))
-        self.__check_attr("single_dataset__about", (str, type(None)))
+        self.check_attr("single_dataset__about", (str, type(None)))
-        self.__check_attr("single_dataset__obs_names", (str, type(None)))
+        self.check_attr("single_dataset__obs_names", (str, type(None)))
-        self.__check_attr("single_dataset__var_names", (str, type(None)))
+        self.check_attr("single_dataset__var_names", (str, type(None)))
 
         if self.single_dataset__datapath is None:
             if self.multi_dataset__dataroot is None:
@@ -357,7 +513,7 @@ class AppConfig(object):
             self.matrix_data_cache_manager = MatrixDataCacheManager(max_cached=1, timelimit_s=None)
 
         # preload this data set
-        matrix_data_loader = MatrixDataLoader(self.single_dataset__datapath, app_config=self)
+        matrix_data_loader = MatrixDataLoader(self.single_dataset__datapath, app_config=self.app_config)
         try:
             matrix_data_loader.pre_load_validation()
         except DatasetAccessError as e:
@@ -388,26 +544,46 @@ class AppConfig(object):
                 )
 
     def handle_multi_dataset(self, context):
-        self.__check_attr("multi_dataset__dataroot", (type(None), dict, str))
+        self.check_attr("multi_dataset__dataroot", (type(None), dict, str))
-        self.__check_attr("multi_dataset__index", (type(None), bool, str))
+        self.check_attr("multi_dataset__index", (type(None), bool, str))
-        self.__check_attr("multi_dataset__allowed_matrix_types", list)
+        self.check_attr("multi_dataset__allowed_matrix_types", list)
-        self.__check_attr("multi_dataset__matrix_cache__max_datasets", int)
+        self.check_attr("multi_dataset__matrix_cache__max_datasets", int)
-        self.__check_attr("multi_dataset__matrix_cache__timelimit_s", (type(None), int, float))
+        self.check_attr("multi_dataset__matrix_cache__timelimit_s", (type(None), int, float))
 
         if self.multi_dataset__dataroot is None:
             return
 
         if type(self.multi_dataset__dataroot) == str:
-            self.multi_dataset__dataroot = dict(d=self.multi_dataset__dataroot)
+            default_dict = dict(base_url="d", dataroot=self.multi_dataset__dataroot)
+            self.multi_dataset__dataroot = dict(d=default_dict)
 
-        for key in self.multi_dataset__dataroot.keys():
+        for tag, dataroot_dict in self.multi_dataset__dataroot.items():
-            # sanity check for well formed keys
+            if "base_url" not in dataroot_dict:
-            if type(key) != str:
+                raise ConfigurationError(f"error in multi_dataset__dataroot: missing base_url for tag {tag}")
-                raise ConfigurationError(f"error in multi_dataset__dataroot {key}")
+            if "dataroot" not in dataroot_dict:
-            if quote_plus(key) != key:
+                raise ConfigurationError(f"error in multi_dataset__dataroot: missing dataroot, for tag {tag}")
-                raise ConfigurationError(f"error in multi_dataset__dataroot {key}")
+
-            if os.path.split(os.path.normpath(key))[-1] != key:
+            base_url = dataroot_dict["base_url"]
-                raise ConfigurationError(f"error in multi_dataset__dataroot {key}")
+
+            # sanity check for well formed base urls
+            bad = False
+            if type(base_url) != str:
+                bad = True
+            elif os.path.normpath(base_url) != base_url:
+                bad = True
+            else:
+                base_url_parts = base_url.split("/")
+                if [quote_plus(part) for part in base_url_parts] != base_url_parts:
+                    bad = True
+                if ".." in base_url_parts:
+                    bad = True
+            if bad:
+                raise ConfigurationError(f"error in multi_dataset__dataroot base_url {base_url} for tag {tag}")
+
+        # verify all the base_urls are unique
+        base_urls = [d["base_url"] for d in self.multi_dataset__dataroot.values()]
+        if len(base_urls) > len(set(base_urls)):
+            raise ConfigurationError("error in multi_dataset__dataroot:  base_urls must be unique")
 
         # error checking
         for mtype in self.multi_dataset__allowed_matrix_types:
@@ -423,13 +599,114 @@ class AppConfig(object):
                 timelimit_s=self.multi_dataset__matrix_cache__timelimit_s,
             )
 
+    def handle_diffexp(self, context):
+        self.check_attr("diffexp__alg_cxg__max_workers", (str, int))
+        self.check_attr("diffexp__alg_cxg__cpu_multiplier", int)
+        self.check_attr("diffexp__alg_cxg__target_workunit", int)
+
+        max_workers = self.diffexp__alg_cxg__max_workers
+        cpu_multiplier = self.diffexp__alg_cxg__cpu_multiplier
+        cpu_count = os.cpu_count()
+        max_workers = min(max_workers, cpu_multiplier * cpu_count)
+        diffexp_tiledb.set_config(max_workers, self.diffexp__alg_cxg__target_workunit)
+
+    def handle_adaptor(self, context):
+        # cxg
+        self.check_attr("adaptor__cxg_adaptor__tiledb_ctx", dict)
+        regionkey = "vfs.s3.region"
+        if regionkey not in self.adaptor__cxg_adaptor__tiledb_ctx:
+            if type(self.data_locator__s3__region_name) == str:
+                self.adaptor__cxg_adaptor__tiledb_ctx[regionkey] = self.data_locator__s3__region_name
+
+        from server.data_cxg.cxg_adaptor import CxgAdaptor
+
+        CxgAdaptor.set_tiledb_context(self.adaptor__cxg_adaptor__tiledb_ctx)
+
+        # anndata
+        self.check_attr("adaptor__anndata_adaptor__backed", bool)
+
+    def handle_limits(self, context):
+        self.check_attr("limits__diffexp_cellcount_max", (type(None), int))
+        self.check_attr("limits__column_request_max", (type(None), int))
+
+    def exceeds_limit(self, limit_name, value):
+        limit_value = getattr(self, "limits__" + limit_name, None)
+        if limit_value is None:  # disabled
+            return False
+        return value > limit_value
+
+
+class DatasetConfig(BaseConfig):
+    """Manages the config attribute associated with a dataset."""
+
+    def __init__(self, tag, app_config, default_config):
+        super().__init__(app_config, default_config)
+        self.tag = tag
+        dc = default_config
+        try:
+            self.app__scripts = dc["app"]["scripts"]
+            self.app__inline_scripts = dc["app"]["inline_scripts"]
+            self.app__about_legal_tos = dc["app"]["about_legal_tos"]
+            self.app__about_legal_privacy = dc["app"]["about_legal_privacy"]
+
+            self.presentation__max_categories = dc["presentation"]["max_categories"]
+            self.presentation__custom_colors = dc["presentation"]["custom_colors"]
+
+            self.user_annotations__enable = dc["user_annotations"]["enable"]
+            self.user_annotations__type = dc["user_annotations"]["type"]
+            self.user_annotations__local_file_csv__directory = dc["user_annotations"]["local_file_csv"]["directory"]
+            self.user_annotations__local_file_csv__file = dc["user_annotations"]["local_file_csv"]["file"]
+            self.user_annotations__ontology__enable = dc["user_annotations"]["ontology"]["enable"]
+            self.user_annotations__ontology__obo_location = dc["user_annotations"]["ontology"]["obo_location"]
+
+            self.embeddings__names = dc["embeddings"]["names"]
+            self.embeddings__enable_reembedding = dc["embeddings"]["enable_reembedding"]
+
+            self.diffexp__enable = dc["diffexp"]["enable"]
+            self.diffexp__lfc_cutoff = dc["diffexp"]["lfc_cutoff"]
+            self.diffexp__top_n = dc["diffexp"]["top_n"]
+
+        except KeyError as e:
+            raise ConfigurationError(f"Unexpected config: {str(e)}")
+
+        # The annotation object is created during complete_config and stored here.
+        self.user_annotations = None
+
+    def complete_config(self, context):
+        self.handle_app(context)
+        self.handle_presentation(context)
+        self.handle_user_annotations(context)
+        self.handle_embeddings(context)
+        self.handle_diffexp(context)
+
+    def handle_app(self, context):
+        self.check_attr("app__scripts", list)
+        self.check_attr("app__inline_scripts", list)
+        self.check_attr("app__about_legal_tos", (type(None), str))
+        self.check_attr("app__about_legal_privacy", (type(None), str))
+
+        # scripts can be string (filename) or dict (attributes).   Convert string to dict.
+        scripts = []
+        for s in self.app__scripts:
+            if isinstance(s, str):
+                scripts.append({"src": s})
+            elif isinstance(s, dict) and isinstance(s["src"], str):
+                scripts.append(s)
+            else:
+                raise ConfigurationError("Scripts must be string or dict")
+        self.app__scripts = scripts
+
+    def handle_presentation(self, context):
+        self.check_attr("presentation__max_categories", int)
+        self.check_attr("presentation__custom_colors", bool)
+
     def handle_user_annotations(self, context):
-        self.__check_attr("user_annotations__enable", bool)
+        self.check_attr("user_annotations__enable", bool)
-        self.__check_attr("user_annotations__type", str)
+        self.check_attr("user_annotations__type", str)
-        self.__check_attr("user_annotations__local_file_csv__directory", (type(None), str))
+        self.check_attr("user_annotations__local_file_csv__directory", (type(None), str))
-        self.__check_attr("user_annotations__local_file_csv__file", (type(None), str))
+        self.check_attr("user_annotations__local_file_csv__file", (type(None), str))
-        self.__check_attr("user_annotations__ontology__enable", bool)
+        self.check_attr("user_annotations__ontology__enable", bool)
-        self.__check_attr("user_annotations__ontology__obo_location", (type(None), str))
+        self.check_attr("user_annotations__ontology__obo_location", (type(None), str))
 
         if self.user_annotations__enable:
             # TODO, replace this with a factory pattern once we have more than one way
@@ -458,8 +735,11 @@ class AppConfig(object):
 
             # if the user has specified a fixed label file, go ahead and validate it
             # so that we can remove errors early in the process.
-            if self.single_dataset__datapath and self.user_annotations__local_file_csv__file:
+            server_config = self.app_config.server_config
-                with self.matrix_data_cache_manager.data_adaptor(self.single_dataset__datapath, self) as data_adaptor:
+            if server_config.single_dataset__datapath and self.user_annotations__local_file_csv__file:
+                with server_config.matrix_data_cache_manager.data_adaptor(
+                    self.tag, server_config.single_dataset__datapath, self.app_config
+                ) as data_adaptor:
                     data_adaptor.check_new_labels(self.user_annotations.read_labels(data_adaptor))
 
             if self.user_annotations__ontology__enable or self.user_annotations__ontology__obo_location:
@@ -487,135 +767,29 @@ class AppConfig(object):
                 )
 
     def handle_embeddings(self, context):
-        self.__check_attr("embeddings__names", list)
+        self.check_attr("embeddings__names", list)
-        self.__check_attr("embeddings__enable_reembedding", bool)
+        self.check_attr("embeddings__enable_reembedding", bool)
 
-        if self.single_dataset__datapath:
+        if self.app_config.server_config.single_dataset__datapath:
             if self.embeddings__enable_reembedding:
-                matrix_data_loader = MatrixDataLoader(self.single_dataset__datapath, app_config=self)
+                matrix_data_loader = MatrixDataLoader(self.single_dataset__datapath, app_config=self.app_config)
                 if matrix_data_loader.matrix_data_type() != MatrixDataType.H5AD:
                     raise ConfigurationError("'enable-reembedding is only supported with H5AD files.")
                 if self.adaptor__anndata_adaptor__backed:
                     raise ConfigurationError("enable-reembedding is not supported when run in --backed mode.")
 
     def handle_diffexp(self, context):
-        self.__check_attr("diffexp__enable", bool)
+        self.check_attr("diffexp__enable", bool)
-        self.__check_attr("diffexp__lfc_cutoff", float)
+        self.check_attr("diffexp__lfc_cutoff", float)
-        self.__check_attr("diffexp__top_n", int)
+        self.check_attr("diffexp__top_n", int)
-        self.__check_attr("diffexp__alg_cxg__max_workers", (str, int))
-        self.__check_attr("diffexp__alg_cxg__cpu_multiplier", int)
-        self.__check_attr("diffexp__alg_cxg__target_workunit", int)
 
-        if self.single_dataset__datapath:
+        server_config = self.app_config.server_config
-            with self.matrix_data_cache_manager.data_adaptor(self.single_dataset__datapath, self) as data_adaptor:
+        if server_config.single_dataset__datapath:
+            with server_config.matrix_data_cache_manager.data_adaptor(
+                self.tag, server_config.single_dataset__datapath, self.app_config
+            ) as data_adaptor:
                 if self.diffexp__enable and data_adaptor.parameters.get("diffexp_may_be_slow", False):
                     context["messagefn"](
                         "CAUTION: due to the size of your dataset, "
                         "running differential expression may take longer or fail."
                     )
-
-        max_workers = self.diffexp__alg_cxg__max_workers
-        cpu_multiplier = self.diffexp__alg_cxg__cpu_multiplier
-        cpu_count = os.cpu_count()
-        max_workers = min(max_workers, cpu_multiplier * cpu_count)
-        diffexp_tiledb.set_config(max_workers, self.diffexp__alg_cxg__target_workunit)
-
-    def handle_adaptor(self, context):
-        # cxg
-        self.__check_attr("adaptor__cxg_adaptor__tiledb_ctx", dict)
-        regionkey = "vfs.s3.region"
-        if regionkey not in self.adaptor__cxg_adaptor__tiledb_ctx:
-            if type(self.data_locator__s3__region_name) == str:
-                self.adaptor__cxg_adaptor__tiledb_ctx[regionkey] = self.data_locator__s3__region_name
-
-        from server.data_cxg.cxg_adaptor import CxgAdaptor
-
-        CxgAdaptor.set_tiledb_context(self.adaptor__cxg_adaptor__tiledb_ctx)
-
-        # anndata
-        self.__check_attr("adaptor__anndata_adaptor__backed", bool)
-
-    def handle_limits(self, context):
-        self.__check_attr("limits__diffexp_cellcount_max", (type(None), int))
-        self.__check_attr("limits__column_request_max", (type(None), int))
-
-    def get_title(self, data_adaptor):
-        return self.single_dataset__title if self.single_dataset__title else data_adaptor.get_title()
-
-    def get_about(self, data_adaptor):
-        return self.single_dataset__about if self.single_dataset__about else data_adaptor.get_about()
-
-    def get_client_config(self, data_adaptor, annotation=None):
-        """
-        Return the configuration as required by the /config REST route
-        """
-
-        # FIXME The current set of config is not consistently presented:
-        # we have camalCase, hyphen-text, and underscore_text
-
-        # make sure the configuration has been checked.
-        self.check_config()
-
-        # features
-        features = [f.todict() for f in data_adaptor.get_features(annotation)]
-
-        # display_names
-        title = self.get_title(data_adaptor)
-        about = self.get_about(data_adaptor)
-
-        display_names = dict(engine=data_adaptor.get_name(), dataset=title)
-
-        # library_versions
-        library_versions = {}
-        library_versions.update(data_adaptor.get_library_versions())
-        library_versions["cellxgene"] = cellxgene_version
-
-        # links
-        links = {"about-dataset": about}
-
-        # parameters
-        parameters = {
-            "layout": self.embeddings__names,
-            "max-category-items": self.presentation__max_categories,
-            "obs_names": self.single_dataset__obs_names,
-            "var_names": self.single_dataset__var_names,
-            "diffexp_lfc_cutoff": self.diffexp__lfc_cutoff,
-            "backed": self.adaptor__anndata_adaptor__backed,
-            "disable-diffexp": not self.diffexp__enable,
-            "enable-reembedding": self.embeddings__enable_reembedding,
-            "annotations": False,
-            "annotations_file": None,
-            "annotations_dir": None,
-            "annotations_cell_ontology_enabled": False,
-            "annotations_cell_ontology_obopath": None,
-            "annotations_cell_ontology_terms": None,
-            "custom_colors": self.presentation__custom_colors,
-            "diffexp-may-be-slow": False,
-            "about_legal_tos": self.server__about_legal_tos,
-            "about_legal_privacy": self.server__about_legal_privacy,
-        }
-
-        data_adaptor.update_parameters(parameters)
-        if annotation:
-            annotation.update_parameters(parameters, data_adaptor)
-
-        # gather it all together
-        c = {}
-        config = c["config"] = {}
-        config["features"] = features
-        config["displayNames"] = display_names
-        config["library_versions"] = library_versions
-        config["links"] = links
-        config["parameters"] = parameters
-        config["limits"] = {
-            "column_request_max": self.limits__column_request_max,
-            "diffexp_cellcount_max": self.limits__diffexp_cellcount_max,
-        }
-
-        return c
-
-    def exceeds_limit(self, limit_name, value):
-        limit_value = getattr(self, "limits__" + limit_name, None)
-        if limit_value is None:  # disabled
-            return False
-        return value > limit_value

server/common/default_config.py

@@ -1,129 +1,159 @@
 import yaml
 
 default_config = """
-# cellxgene configuration
-
 server:
-  verbose: false
+  app:
-  debug: false
+    verbose: false
-  host: "127.0.0.1"
+    debug: false
-  port : null
+    host: "127.0.0.1"
+    port : null
+    open_browser: false
+    force_https: false
+    flask_secret_key: null
+    generate_cache_control_headers: false
+    server_timing_headers: false
+    csp_directives: null
 
-  # Scripts can be a list of either file names (string) or dicts containing keys src, integrity and crossorigin.
+  multi_dataset:
-  # these will be injected into the index template as script tags with these attributes set.
+    # If dataroot is set, then cellxgene may serve multiple datasets.  This parameter is not
-  scripts: []
+    # compatible with single_dataset/datapath.
-  # Inline scripts are a list of file names, where the contents of the file will be injected into the index.
+    # dataroot may be a string, representing the path to a directory or S3 prefix.  In this
-  inline_scripts: []
+    # case the datasets in that location are accessed from <server>/d/<datasetname>.
+    # example:
+    #     dataroot:  /path/to/datasets/
+    # or
+    #     dataroot:  s3://bucket/prefix/
+    #
+    # As an alternative, dataroot can be a dictionary, where a dataset key is associated with a base_url
+    # and a dataroot.
+    # example:
+    #     dataroot:
+    #         d1:
+    #            base_url: set1
+    #            dataroot: /path/to/set1_datasets/
+    #         d2:
+    #            base_url: set2/subdir
+    #            dataroot: /path/to/set2_datasets/
+    #
+    # In this case, datasets can be accessed from <server>/set1/<datasetname> or
+    # <server>/set2/subdir/<datasetname>.  It is possible to have different dataset configurations
+    # for datasets accessed through different dataroots.  For example, in one dataroot, the
+    # user annotations could be enabled, and in another dataroot they could be disabled.
+    # To specify dataroot configurations, add a new top level dictionary to the config named
+    # per_dataset_config. Within per_dataset_config create a dictionary for each dataroot to specialize
+    # ("d1" or "d2" from the example).  Each of these dictionaries has the exact same form as the "dataset"
+    # dictionary (see below).
+    # When this approach is used, the values for each configuration option are checked in
+    # this order: per_dataset_config/<key>, dataset, then the default values.
+    #
+    # example:
+    #
+    # per_dataset_config:
+    #    d1:
+    #       user_annotations:
+    #           enable:  false
+    #    d2:
+    #       user_annotations:
+    #           enable:  true
 
-  open_browser: false
+    dataroot: null
-  about_legal_tos: null
-  about_legal_privacy: null
-  force_https: false
-  flask_secret_key: null
-  generate_cache_control_headers: false
-  server_timing_headers: false
-  csp_directives: null
 
-presentation:
+    # The index page when in multi-dataset mode:
-  max_categories: 1000
+    #   false or null:  this returns a 404 code
-  custom_colors: true
+    #   true:  loads a test index page, which links to the datasets that are available in the dataroot
+    #   string/URL:  redirect to this URL:  flask.redirect(config.multi_dataset__index)
+    index: false
 
-multi_dataset:
+    # A list of allowed matrix types.  If an empty list, then all matrix types are allowed
-  # If dataroot is set, then cellxgene may serve multiple datasets.  This parameter is not
+    allowed_matrix_types: []
-  # compatable with single_dataset/datapath.
-  # dataroot may be a string, representing the path to a directory or S3 prefix.  In this
-  # case the datasets in that location are accessed from <server>/d/<datasetname>.
-  # example:
-  #     dataroot:  /path/to/datasets/
-  # or
-  #     dataroot:  s3://bucket/prefix/
-  #
-  # As an alternative, dataroot can be a dictionary, mapping url prefixes to dataroot paths.
-  # example:
-  #     dataroot:
-  #         set1 : /path/to/set1_datasets/
-  #         set2 : /path/to/set2_datasets/
-  # In this case, datasets can be accessed from <server>/set1/<datasetname> or
-  # <server>/set2/<datasetname>.
 
-  dataroot: null
+    matrix_cache:
+      # The maximum number of datasets that may be opened at one time.  The least recently used dataset
+      # is evicted from the cache first.
+      max_datasets: 5
 
-  # The index page when in multi-dataset mode:
+      # A matrix is automatically removed from the cache after timelimit_s number of seconds.
-  #   false or null:  this returns a 404 code
+      # If timelimit_s is set to None, then there is no time limit.
-  #   true:  loads a test index page, which links to the datasets that are available in the dataroot
+      timelimit_s: 30
-  #   string/URL:  redirect to this URL:  flask.redirect(config.multi_dataset__index)
-  index: false
 
-  # A list of allowed matrix types.  If an empty list, then all matrix types are allowed
+  single_dataset:
-  allowed_matrix_types: []
+    # If datapath is set, then cellxgene with serve a single dataset located at datapath.  This parameter is not
+    # compatible with multi_dataset/dataroot.
+    datapath: null
+    obs_names: null
+    var_names: null
+    about: null
+    title: null
 
-  matrix_cache:
+  diffexp:
-    # The maximum number of datasets that may be opened at one time.  The least recently used dataset
+    alg_cxg:
-    # is evicted from the cache first.
+      # The number of threads to use is computed from: min(max_workers, cpu_multipler * cpu_count).
-    max_datasets: 5
+      # Where cpu_count is determined at runtime.
+      max_workers: 64
+      cpu_multiplier: 4
 
-    # A matrix is automatically removed from the cache after timelimit_s number of seconds.
+      # The target number of matrix elements that are evaluated
-    # If timelimit_s is set to None, then there is no time limit.
+      # together in one thread.
-    timelimit_s: 30
+      target_workunit: 16_000_000
 
-single_dataset:
+  data_locator:
-  datapath: null
+    s3:
-  obs_names: null
+      # s3 region name.
-  var_names: null
+      #   if true, then the s3 location is automatically determined from the datapath or dataroot.
-  about: null
+      #   if false/null, then do not set.
-  title: null
+      #   if a string, then use that value (e.g. us-east-1).
+      region_name: true
 
-user_annotations:
+  adaptor:
-  enable: true
+    cxg_adaptor:
-  type: local_file_csv
+      # The key/values under tiledb_ctx will be used to initialize the tiledb Context.
-  local_file_csv:
+      # If 'vfs.s3.region' is not set, then it will automatically use the setting from
-    directory: null
+      # data_locator / s3 / region_name.
-    file: null
+      tiledb_ctx:
-  ontology:
+        sm.tile_cache_size:  8589934592
-    enable: false
+        sm.num_reader_threads:  32
-    obo_location: null
 
-embeddings:
+    anndata_adaptor:
-  names : []
-  enable_reembedding: false
-
-diffexp:
-  enable: true
-  lfc_cutoff: 0.01
-  top_n: 10
-  alg_cxg:
-    # The number of threads to use is computed from: min(max_workers, cpu_multipler * cpu_count).
-    # Where cpu_count is determined at runtime.
-    max_workers: 64
-    cpu_multiplier: 4
-
-    # The target number of matrix elements that are evaluated
-    # together in one thread.
-    target_workunit: 16_000_000
-
-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:
-  cxg_adaptor:
-    # The key/values under tiledb_ctx will be used to initialize the tiledb Context.
-    # If 'vfs.s3.region' is not set, then it will automatically use the setting from
-    # data_locator / s3 / region_name.
-    tiledb_ctx:
-      sm.tile_cache_size:  8589934592
-      sm.num_reader_threads:  32
-
-  anndata_adaptor:
       backed: false
 
-limits:
+  limits:
-  column_request_max: 32
+    column_request_max: 32
-  diffexp_cellcount_max: null
+    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: []
+
+    about_legal_tos: null
+    about_legal_privacy: null
+
+  presentation:
+    max_categories: 1000
+    custom_colors: true
+
+  user_annotations:
+    enable: true
+    type: local_file_csv
+    local_file_csv:
+      directory: null
+      file: null
+    ontology:
+      enable: false
+      obo_location: null
+
+  embeddings:
+    names : []
+    enable_reembedding: false
+
+  diffexp:
+    enable: true
+    lfc_cutoff: 0.01
+    top_n: 10
 
 """
 

server/common/health.py

@@ -24,10 +24,12 @@ def health_check(config):
     health = {"status": None, "version": "1", "releaseID": cellxgene_version}
 
     checks = False
-    if config.single_dataset__datapath is not None:
+    server_config = config.server_config
-        checks = _is_accessible(config.single_dataset__datapath, config)
+    if config.is_multi_dataset():
-    elif config.multi_dataset__dataroot is not None:
+        dataroots = [datapath_dict["dataroot"] for datapath_dict in server_config.multi_dataset__dataroot.values()]
-        checks = all([_is_accessible(datapath, config) for datapath in config.multi_dataset__dataroot.values()])
+        checks = all([_is_accessible(dataroot, server_config) for dataroot in dataroots])
+    else:
+        checks = _is_accessible(server_config.single_dataset__datapath, server_config)
 
     health["status"] = "pass" if checks else "fail"
     code = HTTPStatus.OK if health["status"] == "pass" else HTTPStatus.BAD_REQUEST

server/common/rest.py

@@ -97,12 +97,13 @@ def _query_parameter_to_filter(args):
     return result
 
 
-def schema_get_helper(data_adaptor, annotations):
+def schema_get_helper(data_adaptor):
     """helper function to gather the schema from the data source and annotations"""
     schema = data_adaptor.get_schema()
     schema = copy.deepcopy(schema)
 
     # add label obs annotations as needed
+    annotations = data_adaptor.dataset_config.user_annotations
     if annotations is not None:
         label_schema = annotations.get_schema(data_adaptor)
         schema["annotations"]["obs"]["columns"].extend(label_schema)
@@ -110,20 +111,20 @@ def schema_get_helper(data_adaptor, annotations):
     return schema
 
 
-def schema_get(data_adaptor, annotations):
+def schema_get(data_adaptor):
-    schema = schema_get_helper(data_adaptor, annotations)
+    schema = schema_get_helper(data_adaptor)
     return make_response(jsonify({"schema": schema}), HTTPStatus.OK)
 
 
-def config_get(app_config, data_adaptor, annotations):
+def config_get(app_config, data_adaptor):
-    config = app_config.get_client_config(data_adaptor, annotations)
+    config = app_config.get_client_config(data_adaptor)
     return make_response(jsonify(config), HTTPStatus.OK)
 
 
-def annotations_obs_get(request, data_adaptor, annotations):
+def annotations_obs_get(request, data_adaptor):
     fields = request.args.getlist("annotation-name", None)
     num_columns_requested = len(data_adaptor.get_obs_keys()) if len(fields) == 0 else len(fields)
-    if data_adaptor.config.exceeds_limit("column_request_max", num_columns_requested):
+    if data_adaptor.server_config.exceeds_limit("column_request_max", num_columns_requested):
         return abort(HTTPStatus.BAD_REQUEST)
     preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
     if preferred_mimetype != "application/octet-stream":
@@ -131,6 +132,7 @@ def annotations_obs_get(request, data_adaptor, annotations):
 
     try:
         labels = None
+        annotations = data_adaptor.dataset_config.user_annotations
         if annotations:
             labels = annotations.read_labels(data_adaptor)
         fbs = data_adaptor.annotation_to_fbs_matrix(Axis.OBS, fields, labels)
@@ -139,8 +141,9 @@ def annotations_obs_get(request, data_adaptor, annotations):
         return abort_and_log(HTTPStatus.BAD_REQUEST, str(e), include_exc_info=True)
 
 
-def annotations_put_fbs_helper(data_adaptor, annotations, fbs):
+def annotations_put_fbs_helper(data_adaptor, fbs):
     """helper function to write annotations from fbs"""
+    annotations = data_adaptor.dataset_config.user_annotations
     if annotations is None:
         raise DisabledFeatureError("Writable annotations are not enabled")
 
@@ -150,7 +153,8 @@ def annotations_put_fbs_helper(data_adaptor, annotations, fbs):
     annotations.write_labels(new_label_df, data_adaptor)
 
 
-def annotations_obs_put(request, data_adaptor, annotations):
+def annotations_obs_put(request, data_adaptor):
+    annotations = data_adaptor.dataset_config.user_annotations
     if annotations is None:
         return abort(HTTPStatus.NOT_IMPLEMENTED)
 
@@ -163,17 +167,17 @@ def annotations_obs_put(request, data_adaptor, annotations):
         annotations.set_collection(anno_collection)
 
     try:
-        annotations_put_fbs_helper(data_adaptor, annotations, fbs)
+        annotations_put_fbs_helper(data_adaptor, fbs)
         res = json.dumps({"status": "OK"})
         return make_response(res, HTTPStatus.OK, {"Content-Type": "application/json"})
     except (ValueError, DisabledFeatureError, KeyError) as e:
         return abort_and_log(HTTPStatus.BAD_REQUEST, str(e), include_exc_info=True)
 
 
-def annotations_var_get(request, data_adaptor, annotations):
+def annotations_var_get(request, data_adaptor):
     fields = request.args.getlist("annotation-name", None)
     num_columns_requested = len(data_adaptor.get_var_keys()) if len(fields) == 0 else len(fields)
-    if data_adaptor.config.exceeds_limit("column_request_max", num_columns_requested):
+    if data_adaptor.server_config.exceeds_limit("column_request_max", num_columns_requested):
         return abort(HTTPStatus.BAD_REQUEST)
     preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
     if preferred_mimetype != "application/octet-stream":
@@ -181,6 +185,7 @@ def annotations_var_get(request, data_adaptor, annotations):
 
     try:
         labels = None
+        annotations = data_adaptor.dataset_config.user_annotations
         if annotations is not None:
             labels = annotations.read_labels(data_adaptor)
         return make_response(
@@ -226,7 +231,7 @@ def data_var_get(request, data_adaptor):
 
 
 def colors_get(data_adaptor):
-    if not data_adaptor.config.presentation__custom_colors:
+    if not data_adaptor.dataset_config.presentation__custom_colors:
         return make_response(jsonify({}), HTTPStatus.OK)
     try:
         return make_response(jsonify(data_adaptor.get_colors()), HTTPStatus.OK)
@@ -235,7 +240,7 @@ def colors_get(data_adaptor):
 
 
 def diffexp_obs_post(request, data_adaptor):
-    if not data_adaptor.config.diffexp__enable:
+    if not data_adaptor.dataset_config.diffexp__enable:
         return abort(HTTPStatus.NOT_IMPLEMENTED)
 
     args = request.get_json()
@@ -273,7 +278,7 @@ def diffexp_obs_post(request, data_adaptor):
 def layout_obs_get(request, data_adaptor):
     fields = request.args.getlist("layout-name", None)
     num_columns_requested = len(data_adaptor.get_embedding_names()) if len(fields) == 0 else len(fields)
-    if data_adaptor.config.exceeds_limit("column_request_max", num_columns_requested):
+    if data_adaptor.server_config.exceeds_limit("column_request_max", num_columns_requested):
         return abort(HTTPStatus.BAD_REQUEST)
 
     preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
@@ -296,7 +301,7 @@ def layout_obs_get(request, data_adaptor):
 
 
 def layout_obs_put(request, data_adaptor):
-    if not data_adaptor.config.embedding__enable_reembedding:
+    if not data_adaptor.dataset_config.embedding__enable_reembedding:
         return abort(HTTPStatus.NOT_IMPLEMENTED)
 
     preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])

server/data_anndata/anndata_adaptor.py

@@ -28,10 +28,9 @@ def anndata_version_is_pre_070():
 
 
 class AnndataAdaptor(DataAdaptor):
-    def __init__(self, data_locator, config=None):
+    def __init__(self, data_locator, app_config=None, dataset_config=None):
-        super().__init__(config)
+        super().__init__(data_locator, app_config, dataset_config)
         self.data = None
-        self.data_locator = data_locator
         self._load_data(data_locator)
         self._validate_and_initialize()
 
@@ -55,14 +54,8 @@ class AnndataAdaptor(DataAdaptor):
         return data_locator.size() if data_locator.islocal() else 0
 
     @staticmethod
-    def open(data_locator, config):
+    def open(data_locator, app_config, dataset_config=None):
-        return AnndataAdaptor(data_locator, config)
+        return AnndataAdaptor(data_locator, app_config, dataset_config)
-
-    def get_location(self):
-        return self.data_locator.uri_or_path
-
-    def get_data_locator(self):
-        return self.data_locator
 
     def get_name(self):
         return "cellxgene anndata adaptor version"
@@ -100,7 +93,7 @@ class AnndataAdaptor(DataAdaptor):
         for (ax_name, var_name) in ((Axis.OBS, "obs"), (Axis.VAR, "var")):
             config_name = f"single_dataset__{var_name}_names"
             parameter_name = f"{var_name}_names"
-            name = getattr(self.config, config_name)
+            name = getattr(self.server_config, config_name)
             df_axis = getattr(self.data, str(ax_name))
             if name is None:
                 # Default: create unique names from index
@@ -161,7 +154,7 @@ class AnndataAdaptor(DataAdaptor):
             with data_locator.local_handle() as lh:
                 # as of AnnData 0.6.19, backed mode performs initial load fast, but at the
                 # cost of significantly slower access to X data.
-                backed = "r" if self.config.adaptor__anndata_adaptor__backed else None
+                backed = "r" if self.server_config.adaptor__anndata_adaptor__backed else None
                 self.data = anndata.read_h5ad(lh, backed=backed)
 
         except ValueError:
@@ -181,7 +174,7 @@ class AnndataAdaptor(DataAdaptor):
             )
 
     def _validate_and_initialize(self):
-        if anndata_version_is_pre_070() and self.config.adaptor__anndata_adaptor__backed:
+        if anndata_version_is_pre_070() and self.server_config.adaptor__anndata_adaptor__backed:
             warnings.warn(
                 "Use of --backed mode with anndata versions older than 0.7 will have serious "
                 "performance issues. Please update to at least anndata 0.7 or later."
@@ -199,7 +192,7 @@ class AnndataAdaptor(DataAdaptor):
 
         # heuristic
         n_values = self.data.shape[0] * self.data.shape[1]
-        if (n_values > 1e8 and self.config.adaptor__anndata_adaptor__backed is True) or (n_values > 5e8):
+        if (n_values > 1e8 and self.server_config.adaptor__anndata_adaptor__backed is True) or (n_values > 5e8):
             self.parameters.update({"diffexp_may_be_slow": True})
 
     def _is_valid_layout(self, arr):
@@ -246,7 +239,7 @@ class AnndataAdaptor(DataAdaptor):
                     )
                 if isinstance(datatype, CategoricalDtype):
                     category_num = len(curr_axis[ann].dtype.categories)
-                    if category_num > 500 and category_num > self.config.presentation__max_categories:
+                    if category_num > 500 and category_num > self.dataset_config.presentation__max_categories:
                         warnings.warn(
                             f"{str(ax).title()} annotation '{ann}' has {category_num} categories, this may be "
                             f"cumbersome or slow to display. We recommend setting the "
@@ -277,7 +270,7 @@ class AnndataAdaptor(DataAdaptor):
             c) cap total list of layouts at global const MAX_LAYOUTS
         """
         # load default layouts from the data.
-        layouts = self.config.embeddings__names
+        layouts = self.dataset_config.embeddings__names
 
         if layouts is None or len(layouts) == 0:
             layouts = [key[2:] for key in self.data.obsm_keys() if type(key) == str and key.startswith("X_")]
@@ -329,9 +322,9 @@ class AnndataAdaptor(DataAdaptor):
 
     def compute_diffexp_ttest(self, maskA, maskB, top_n=None, lfc_cutoff=None):
         if top_n is None:
-            top_n = self.config.diffexp__top_n
+            top_n = self.dataset_config.diffexp__top_n
         if lfc_cutoff is None:
-            lfc_cutoff = self.config.diffexp__lfc_cutoff
+            lfc_cutoff = self.dataset_config.diffexp__lfc_cutoff
         return diffexp_generic.diffexp_ttest(self, maskA, maskB, top_n, lfc_cutoff)
 
     def get_colors(self):
@@ -355,7 +348,7 @@ class AnndataAdaptor(DataAdaptor):
         return getattr(self.data.obs, term_name)
 
     def get_obs_index(self):
-        name = self.config.single_dataset__obs_names
+        name = self.server_config.single_dataset__obs_names
         if name is None:
             return self.original_obs_index
         else:

server/data_common/data_adaptor.py

@@ -14,12 +14,17 @@ from server.common.app_config import AppFeature, AppConfig
 class DataAdaptor(metaclass=ABCMeta):
     """Base class for loading and accessing matrix data"""
 
-    def __init__(self, config):
+    def __init__(self, data_locator, app_config, dataset_config=None):
-        if type(config) != AppConfig:
+        if type(app_config) != AppConfig:
             raise TypeError("config expected to be of type AppConfig")
 
+        # location to the dataset
+        self.data_locator = data_locator
+
         # config is the application configuration
-        self.config = config
+        self.app_config = app_config
+        self.server_config = self.app_config.server_config
+        self.dataset_config = dataset_config or app_config.default_dataset_config
 
         # parameters set by this data adaptor based on the data.
         self.parameters = {}
@@ -31,7 +36,7 @@ class DataAdaptor(metaclass=ABCMeta):
 
     @staticmethod
     @abstractmethod
-    def open(data_locator, config):
+    def open(data_locator, app_config, dataset_config):
         pass
 
     @staticmethod
@@ -109,13 +114,11 @@ class DataAdaptor(metaclass=ABCMeta):
     def cleanup(self):
         pass
 
-    @abstractmethod
-    def get_location(self):
-        pass
-
-    @abstractmethod
     def get_data_locator(self):
-        pass
+        return self.data_locator
+
+    def get_location(self):
+        return self.data_locator.uri_or_path
 
     def get_about(self):
         return None
@@ -149,8 +152,8 @@ class DataAdaptor(metaclass=ABCMeta):
         features = [
             AppFeature("/cluster/", method="POST", available=False),
             AppFeature("/layout/obs", method="GET", available=self.get_embedding_names() is not None),
-            AppFeature("/layout/obs", method="PUT", available=self.config.embeddings__enable_reembedding),
+            AppFeature("/layout/obs", method="PUT", available=self.dataset_config.embeddings__enable_reembedding),
-            AppFeature("/diffexp/", method="POST", available=self.config.diffexp__enable),
+            AppFeature("/diffexp/", method="POST", available=self.dataset_config.diffexp__enable),
             AppFeature("/annotations/obs", method="PUT", available=annotations is not None),
         ]
         return features
@@ -260,7 +263,6 @@ class DataAdaptor(metaclass=ABCMeta):
         * currently only supports access on VAR axis
         * currently only supports filtering on VAR axis
         """
-
         if axis != Axis.VAR:
             raise ValueError("Only VAR dimension access is supported")
 
@@ -273,7 +275,7 @@ class DataAdaptor(metaclass=ABCMeta):
             raise FilterError("filtering on obs unsupported")
 
         num_columns = self.get_shape()[1] if var_selector is None else np.count_nonzero(var_selector)
-        if self.config.exceeds_limit("column_request_max", num_columns):
+        if self.server_config.exceeds_limit("column_request_max", num_columns):
             raise ExceedsLimitError("Requested dataframe columns exceed column request limit")
 
         X = self.get_X_array(obs_selector, var_selector)
@@ -301,14 +303,14 @@ class DataAdaptor(metaclass=ABCMeta):
         except (KeyError, IndexError):
             raise FilterError("Error parsing filter")
         if top_n is None:
-            top_n = self.config.diffexp__top_n
+            top_n = self.dataset_config.diffexp__top_n
 
-        if self.config.exceeds_limit(
+        if self.server_config.exceeds_limit(
             "diffexp_cellcount_max", np.count_nonzero(obs_mask_A) + np.count_nonzero(obs_mask_B)
         ):
             raise ExceedsLimitError("Diffexp request exceeds max cell count limit")
 
-        result = self.compute_diffexp_ttest(obs_mask_A, obs_mask_B, top_n, self.config.diffexp__lfc_cutoff)
+        result = self.compute_diffexp_ttest(obs_mask_A, obs_mask_B, top_n, self.dataset_config.diffexp__lfc_cutoff)
 
         try:
             return jsonify_numpy(result)

server/data_common/matrix_loader.py

@@ -29,7 +29,7 @@ class MatrixDataCacheItem(object):
         self.data_lock.r_release()
         return None
 
-    def acquire_and_open(self, app_config):
+    def acquire_and_open(self, app_config, dataset_config=None):
         """returns the data_adaptor if cached.  opens the data_adaptor if not.
         In either case, the a reader lock is taken.  Must call release when
         the data_adaptor is no longer needed"""
@@ -43,7 +43,7 @@ class MatrixDataCacheItem(object):
         if not self.data_adaptor:
             try:
                 self.loader.pre_load_validation()
-                self.data_adaptor = self.loader.open(app_config)
+                self.data_adaptor = self.loader.open(app_config, dataset_config)
             except Exception as e:
                 # necessary to hold the reader lock after an exception, since
                 # the release will occur when the context exits.
@@ -115,7 +115,7 @@ class MatrixDataCacheManager(object):
     # will automatically be refreshed.
 
     def __init__(self, max_cached, timelimit_s=None):
-        # key is location, value is a MatrixDataCacheInfo
+        # key is tuple(url_dataroot, location), value is a MatrixDataCacheInfo
         self.datasets = {}
 
         # lock to protect the datasets
@@ -131,20 +131,21 @@ class MatrixDataCacheManager(object):
         self.timelimit_s = timelimit_s
 
     @contextmanager
-    def data_adaptor(self, location, app_config):
+    def data_adaptor(self, url_dataroot, location, app_config):
         # create a loader for to this location if it does not already exist
 
         delete_adaptor = None
         data_adaptor = None
         cache_item = None
 
+        key = (url_dataroot, location)
         with self.lock:
             self.evict_old_datasets()
-            info = self.datasets.get(location)
+            info = self.datasets.get(key)
             if info is not None:
                 info.last_access = time.time()
                 info.num_access += 1
-                self.datasets[location] = info
+                self.datasets[key] = info
                 data_adaptor = info.cache_item.acquire_existing()
                 cache_item = info.cache_item
 
@@ -165,19 +166,20 @@ class MatrixDataCacheManager(object):
                 loader = MatrixDataLoader(location, app_config=app_config)
                 cache_item = MatrixDataCacheItem(loader)
                 item = MatrixDataCacheInfo(cache_item, time.time())
-                self.datasets[location] = item
+                self.datasets[key] = item
 
         try:
             assert cache_item
             if delete_adaptor:
                 delete_adaptor.delete()
             if data_adaptor is None:
-                data_adaptor = cache_item.acquire_and_open(app_config)
+                dataset_config = app_config.get_dataset_config(url_dataroot)
+                data_adaptor = cache_item.acquire_and_open(app_config, dataset_config)
             yield data_adaptor
         except DatasetAccessError:
             cache_item.release()
             with self.lock:
-                del self.datasets[location]
+                del self.datasets[key]
                 cache_item.delete()
             cache_item = None
             raise
@@ -215,7 +217,7 @@ class MatrixDataType(Enum):
 class MatrixDataLoader(object):
     def __init__(self, location, matrix_data_type=None, app_config=None):
         """ location can be a string or DataLocator """
-        region_name = None if app_config is None else app_config.data_locator__s3__region_name
+        region_name = None if app_config is None else app_config.server_config.data_locator__s3__region_name
         self.location = DataLocator(location, region_name=region_name)
         if not self.location.exists():
             raise DatasetAccessError("Dataset does not exist.", HTTPStatus.NOT_FOUND)
@@ -254,12 +256,12 @@ class MatrixDataLoader(object):
 
         if not app_config:
             return True
-        if not app_config.multi_dataset__dataroot:
+        if not app_config.is_multi_dataset():
             return True
-        if len(app_config.multi_dataset__allowed_matrix_types) == 0:
+        if len(app_config.server_config.multi_dataset__allowed_matrix_types) == 0:
             return True
 
-        for val in app_config.multi_dataset__allowed_matrix_types:
+        for val in app_config.server_config.multi_dataset__allowed_matrix_types:
             try:
                 if self.matrix_data_type == MatrixDataType(val):
                     return True
@@ -279,6 +281,6 @@ class MatrixDataLoader(object):
     def file_size(self):
         return self.matrix_type.file_size(self.location)
 
-    def open(self, app_config):
+    def open(self, app_config, dataset_config=None):
         # create and return a DataAdaptor object
-        return self.matrix_type.open(self.location, app_config)
+        return self.matrix_type.open(self.location, app_config, dataset_config)

server/data_cxg/cxg_adaptor.py

@@ -24,11 +24,10 @@ class CxgAdaptor(DataAdaptor):
         {"sm.tile_cache_size": 8 * 1024 * 1024 * 1024, "sm.num_reader_threads": 32, "vfs.s3.region": "us-east-1"}
     )
 
-    def __init__(self, data_locator, config=None):
+    def __init__(self, data_locator, app_config=None, dataset_config=None):
-        super().__init__(config)
+        super().__init__(data_locator, app_config, dataset_config)
         self.lock = threading.Lock()
 
-        self.data_locator = data_locator
         self.url = data_locator.uri_or_path
         if self.url[-1] != "/":
             self.url += "/"
@@ -66,8 +65,8 @@ class CxgAdaptor(DataAdaptor):
         return 0
 
     @staticmethod
-    def open(data_locator, args):
+    def open(data_locator, app_config, dataset_config=None):
-        return CxgAdaptor(data_locator, args)
+        return CxgAdaptor(data_locator, app_config, dataset_config)
 
     def get_about(self):
         return self.about if self.about else super().get_about()
@@ -75,12 +74,6 @@ class CxgAdaptor(DataAdaptor):
     def get_title(self):
         return self.title if self.title else super().get_title()
 
-    def get_location(self):
-        return self.url
-
-    def get_data_locator(self):
-        return self.data_locator
-
     def get_name(self):
         return "cellxgene cxg adaptor version"
 
@@ -196,9 +189,9 @@ class CxgAdaptor(DataAdaptor):
 
     def compute_diffexp_ttest(self, maskA, maskB, top_n=None, lfc_cutoff=None):
         if top_n is None:
-            top_n = self.config.diffexp__top_n
+            top_n = self.dataset_config.diffexp__top_n
         if lfc_cutoff is None:
-            lfc_cutoff = self.config.diffexp__lfc_cutoff
+            lfc_cutoff = self.dataset_config.diffexp__lfc_cutoff
         return diffexp_cxg.diffexp_ttest(self, maskA, maskB, top_n, lfc_cutoff)
 
     def get_colors(self):

server/eb/Makefile

@@ -11,11 +11,13 @@ clean:
 # Presumes that a top-level `make build-client` has been done to 
 # create the client static assets.
 
+cwd := $(shell pwd)
+
 .PHONY: build
 build: clean
 	mkdir artifact.dir; \
 	(cd ../.. ; \
-	    git ls-files server/ | cpio -pdm server/eb/artifact.dir ; ); \
+	  git ls-files server/ | cpio -pdm $(cwd)/artifact.dir ; ); \
 	$(call copy_client_assets,../../client/build,artifact.dir/server) ; \
 	set -e ; \
 	cp app.py artifact.dir/application.py; \

server/eb/app.py

@@ -58,6 +58,7 @@ class WSGIServer(Server):
     @staticmethod
     def _before_adding_routes(app, app_config):
         script_hashes, style_hashes = WSGIServer.get_csp_hashes(app, app_config)
+        server_config = app_config.server_config
         csp = {
             "default-src": ["'self'"],
             "connect-src": ["'self'"],
@@ -72,14 +73,14 @@ class WSGIServer(Server):
         if not app.debug:
             csp["upgrade-insecure-requests"] = ""
 
-        if app_config.server__csp_directives:
+        if server_config.app__csp_directives:
-            for k, v in app_config.server__csp_directives.items():
+            for k, v in server_config.app__csp_directives.items():
                 if not isinstance(v, list):
                     v = [v]
                 csp[k] = csp.get(k, []) + v
 
         Talisman(
-            app, force_https=app_config.server__force_https, frame_options="DENY", content_security_policy=csp,
+            app, force_https=server_config.app__force_https, frame_options="DENY", content_security_policy=csp,
         )
 
     @staticmethod
@@ -102,16 +103,18 @@ class WSGIServer(Server):
 
     @staticmethod
     def compute_inline_scp_hashes(app, app_config):
-        inline_scripts = app_config.server__inline_scripts
+        dataset_configs = [app_config.default_dataset_config] + list(app_config.dataroot_config.values())
         hashes = []
-        for script in inline_scripts:
+        for dataset_config in dataset_configs:
-            with app.open_resource(f"../common/web/templates/{script}") as f:
+            inline_scripts = dataset_config.app__inline_scripts
-                content = f.read()
+            for script in inline_scripts:
-                # we use jinja2 template include, which trims final newline if present.
+                with app.open_resource(f"../common/web/templates/{script}") as f:
-                if content[-1] == 0x0A:
+                    content = f.read()
-                    content = content[0:-1]
+                    # we use jinja2 template include, which trims final newline if present.
-                hash = base64.b64encode(hashlib.sha256(content).digest())
+                    if content[-1] == 0x0A:
-                hashes.append(f"'sha256-{hash.decode('utf-8')}'")
+                        content = content[0:-1]
+                    hash = base64.b64encode(hashlib.sha256(content).digest())
+                    hashes.append(f"'sha256-{hash.decode('utf-8')}'")
         return hashes
 
     @staticmethod
@@ -156,7 +159,7 @@ try:
     dataroot = os.getenv("CXG_DATAROOT")
     if dataroot:
         logging.info("Configuration from CXG_DATAROOT")
-        app_config.update(multi_dataset__dataroot=dataroot)
+        app_config.update_server_config(multi_dataset__dataroot=dataroot)
 
     secret_name = os.getenv("CXG_AWS_SECRET_NAME")
     if secret_name:
@@ -174,26 +177,23 @@ try:
             sys.exit(1)
 
         flask_secret_key = get_flask_secret_key(secret_region_name, secret_name)
-        app_config.update(server__flask_secret_key=flask_secret_key)
+        app_config.update_server_config(app__flask_secret_key=flask_secret_key)
 
     # features are unsupported in the current hosted server
-    app_config.update(
+    app_config.update_default_dataset_config(
-        user_annotations__enable=False,
+        user_annotations__enable=False, embeddings__enable_reembedding=False,
-        embeddings__enable_reembedding=False,
-        multi_dataset__allowed_matrix_types=["cxg"],
     )
+    app_config.update_server_config(multi_dataset__allowed_matrix_types=["cxg"],)
 
     app_config.complete_config(logging.info)
 
-    if not app_config.server__flask_secret_key:
+    if not app_config.server_config.app__flask_secret_key:
         logging.critical(
             "flask_secret_key is not provided.  Either set in config file, CXG_SECRET_KEY environment variable, "
             "or in AWS Secret Manager"
         )
         sys.exit(1)
 
-    user_annotations = app_config.user_annotations
-
     server = WSGIServer(app_config)
 
     debug = False
@@ -203,10 +203,10 @@ except Exception:
     logging.critical("Caught exception during initialization", exc_info=True)
     sys.exit(1)
 
-if app_config.multi_dataset__dataroot:
+if app_config.is_multi_dataset():
-    logging.info(f"starting server with multi_dataset__dataroot={app_config.multi_dataset__dataroot}")
+    logging.info(f"starting server with multi_dataset__dataroot={app_config.server_config.multi_dataset__dataroot}")
-elif app_config.single_dataset__datapath:
+else:
-    logging.info(f"starting server with single_dataset__datapath={app_config.single_dataset__datapath}")
+    logging.info(f"starting server with single_dataset__datapath={app_config.server_config.single_dataset__datapath}")
 
 if __name__ == "__main__":
     try:

server/test/__init__.py

@@ -27,21 +27,18 @@ def data_with_tmp_annotations(ext: MatrixDataType, annotations_fixture=False):
     annotations_file = path.join(tmp_dir, "test_annotations.csv")
     if annotations_fixture:
         shutil.copyfile(f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k-annotations.csv", annotations_file)
-    args = {
-        "embeddings__names": ["umap"],
-        "presentation__max_categories": 100,
-        "single_dataset__obs_names": None,
-        "single_dataset__var_names": None,
-        "diffexp__lfc_cutoff": 0.01,
-    }
     fname = {
         MatrixDataType.H5AD: f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad",
         MatrixDataType.CXG: "test/test_datasets/pbmc3k.cxg",
     }[ext]
     data_locator = DataLocator(fname)
     config = AppConfig()
-    config.update(**args)
+    config.update_server_config(
-    config.update(single_dataset__datapath=data_locator.path)
+        single_dataset__obs_names=None, single_dataset__var_names=None, single_dataset__datapath=data_locator.path
+    )
+    config.update_default_dataset_config(
+        embeddings__names=["umap"], presentation__max_categories=100, diffexp__lfc_cutoff=0.01,
+    )
     config.complete_config()
     data = MatrixDataLoader(data_locator.abspath()).open(config)
     annotations = AnnotationsLocalFile(None, annotations_file)
@@ -66,21 +63,21 @@ def skip_if(condition, reason: str):
     return decorator
 
 
-def app_config(data_locator, backed=False, extra={}):
+def app_config(data_locator, backed=False, extra_server_config={}, extra_dataset_config={}):
-    args = {
-        "embeddings__names": ["umap", "tsne", "pca"],
-        "presentation__max_categories": 100,
-        "single_dataset__obs_names": None,
-        "single_dataset__var_names": None,
-        "diffexp__lfc_cutoff": 0.01,
-        "adaptor__anndata_adaptor__backed": backed,
-        "single_dataset__datapath": data_locator,
-        "limits__diffexp_cellcount_max": None,
-        "limits__column_request_max": None,
-    }
     config = AppConfig()
-    config.update(**args)
+    config.update_server_config(
-    config.update(**extra)
+        single_dataset__obs_names=None,
+        single_dataset__var_names=None,
+        adaptor__anndata_adaptor__backed=backed,
+        single_dataset__datapath=data_locator,
+        limits__diffexp_cellcount_max=None,
+        limits__column_request_max=None,
+    )
+    config.update_default_dataset_config(
+        embeddings__names=["umap", "tsne", "pca"], presentation__max_categories=100, diffexp__lfc_cutoff=0.01
+    )
+    config.update_server_config(**extra_server_config)
+    config.update_default_dataset_config(**extra_dataset_config)
     config.complete_config()
     return config
 

server/test/run_diffexp.py

@@ -32,8 +32,8 @@ def main():
     args = parser.parse_args()
 
     app_config = AppConfig()
-    app_config.single_dataset__datapath = args.dataset
+    app_config.update_server_config(single_dataset__datapath=args.dataset)
-    app_config.server__verbose = True
+    app_config.update_server_config(app__verbose=True)
     app_config.complete_config()
 
     loader = MatrixDataLoader(args.dataset)

server/test/test_anndata_adaptor.py

@@ -107,9 +107,9 @@ class AdaptorTest(unittest.TestCase):
             self.assertEqual(len(feature), 1)
 
         check_feature("POST", "/cluster/", False)
-        check_feature("POST", "/diffexp/", self.data.config.diffexp__enable)
+        check_feature("POST", "/diffexp/", self.data.dataset_config.diffexp__enable)
         check_feature("GET", "/layout/obs", True)
-        check_feature("PUT", "/layout/obs", self.data.config.embeddings__enable_reembedding)
+        check_feature("PUT", "/layout/obs", self.data.dataset_config.embeddings__enable_reembedding)
         check_feature("PUT", "/annotations/obs", False)
 
     def test_layout(self):

server/test/test_anndata_adaptor_data_load.py

@@ -15,7 +15,7 @@ class DataLoadAdaptorTest(unittest.TestCase):
     def setUp(self):
         self.data_file = DataLocator(f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad")
         config = AppConfig()
-        config.update(single_dataset__datapath=self.data_file.path)
+        config.update_server_config(single_dataset__datapath=self.data_file.path)
         config.complete_config()
         self.data = AnndataAdaptor(self.data_file, config)
 
@@ -40,14 +40,18 @@ class DataLocatorAdaptorTest(unittest.TestCase):
     Test various types of data locators we expect to consume
     """
 
-    def setUp(self):
+    def get_basic_config(self):
-        self.args = {
+        config = AppConfig()
-            "embeddings__names": ["umap"],
+        config.update_server_config(
-            "presentation__max_categories": 100,
+            single_dataset__obs_names=None,
-            "single_dataset__obs_names": None,
+            single_dataset__var_names=None,
-            "single_dataset__var_names": None,
+        )
-            "diffexp__lfc_cutoff": 0.01,
+        config.update_default_dataset_config(
-        }
+            embeddings__names=["umap"],
+            presentation__max_categories=100,
+            diffexp__lfc_cutoff=0.01,
+        )
+        return config
 
     def stdAsserts(self, data):
         """ run these each time we load the data """
@@ -57,9 +61,8 @@ class DataLocatorAdaptorTest(unittest.TestCase):
 
     def test_posix_file(self):
         locator = DataLocator("../example-dataset/pbmc3k.h5ad")
-        config = AppConfig()
+        config = self.get_basic_config()
-        config.update(**self.args)
+        config.update_server_config(single_dataset__datapath=locator.path)
-        config.update(single_dataset__datapath=locator.path)
         config.complete_config()
         data = AnndataAdaptor(locator, config)
         self.stdAsserts(data)
@@ -67,15 +70,13 @@ class DataLocatorAdaptorTest(unittest.TestCase):
     def test_url_https(self):
         url = "https://raw.githubusercontent.com/chanzuckerberg/cellxgene/main/example-dataset/pbmc3k.h5ad"
         locator = DataLocator(url)
-        config = AppConfig()
+        config = self.get_basic_config()
-        config.update(**self.args)
         data = AnndataAdaptor(locator, config)
         self.stdAsserts(data)
 
     def test_url_http(self):
         url = "http://raw.githubusercontent.com/chanzuckerberg/cellxgene/main/example-dataset/pbmc3k.h5ad"
         locator = DataLocator(url)
-        config = AppConfig()
+        config = self.get_basic_config()
-        config.update(**self.args)
         data = AnndataAdaptor(locator, config)
         self.stdAsserts(data)

server/test/test_app_config.py

@@ -11,60 +11,90 @@ import requests
 class AppConfigTest(unittest.TestCase):
     def test_update(self):
         c = AppConfig()
-        c.update(server__verbose=True, multi_dataset__dataroot="datadir")
+        c.update_server_config(app__verbose=True, multi_dataset__dataroot="datadir")
-        v = c.changes_from_default()
+        v = c.server_config.changes_from_default()
-        self.assertCountEqual(v, [("server__verbose", True, False), ("multi_dataset__dataroot", "datadir", None)])
+        self.assertCountEqual(v, [("app__verbose", True, False), ("multi_dataset__dataroot", "datadir", None)])
 
         c = AppConfig()
-        c.update(server__scripts=(), server__inline_scripts=())
+        c.update_default_dataset_config(app__scripts=(), app__inline_scripts=())
-        v = c.changes_from_default()
+        v = c.server_config.changes_from_default()
         self.assertCountEqual(v, [])
 
         c = AppConfig()
-        c.update(server__scripts=[], server__inline_scripts=[])
+        c.update_default_dataset_config(app__scripts=[], app__inline_scripts=[])
-        v = c.changes_from_default()
+        v = c.default_dataset_config.changes_from_default()
         self.assertCountEqual(v, [])
 
         c = AppConfig()
-        c.update(server__scripts=("a", "b"), server__inline_scripts=["c", "d"])
+        c.update_default_dataset_config(app__scripts=("a", "b"), app__inline_scripts=["c", "d"])
-        v = c.changes_from_default()
+        v = c.default_dataset_config.changes_from_default()
-        self.assertCountEqual(v, [("server__scripts", ["a", "b"], []), ("server__inline_scripts", ["c", "d"], [])])
+        self.assertCountEqual(v, [("app__scripts", ["a", "b"], []), ("app__inline_scripts", ["c", "d"], [])])
 
     def test_multi_dataset(self):
 
         c = AppConfig()
         # test for illegal url_dataroots
-        for illegal in ("a/b", "../b", "!$*", "\\n", "", "(bad)"):
+        for illegal in ("../b", "!$*", "\\n", "", "(bad)"):
-            c.update(multi_dataset__dataroot={illegal: f"{PROJECT_ROOT}/example-dataset"})
+            c.update_server_config(
+                multi_dataset__dataroot={"tag": {"base_url": illegal, "dataroot": "{PROJECT_ROOT}/example-dataset"}}
+            )
             with self.assertRaises(ConfigurationError):
                 c.complete_config()
 
         # test for legal url_dataroots
-        for legal in (
+        for legal in ("d", "this.is-okay_", "a/b"):
-            "d",
+            c.update_server_config(
-            "this.is-okay_",
+                multi_dataset__dataroot={"tag": {"base_url": legal, "dataroot": "{PROJECT_ROOT}/example-dataset"}}
-        ):
+            )
-            c.update(multi_dataset__dataroot={legal: f"{PROJECT_ROOT}/example-dataset"})
             c.complete_config()
 
         # test that multi dataroots work end to end
-        c.update(
+        c.update_server_config(
             multi_dataset__dataroot=dict(
-                set1=f"{PROJECT_ROOT}/example-dataset", set2=f"{PROJECT_ROOT}/server/test/test_datasets"
+                s1=dict(dataroot=f"{PROJECT_ROOT}/example-dataset", base_url="set1/1/2"),
+                s2=dict(dataroot=f"{PROJECT_ROOT}/server/test/test_datasets", base_url="set2"),
+                s3=dict(dataroot=f"{PROJECT_ROOT}/server/test/test_datasets", base_url="set3"),
             )
         )
+
+        # Change this default to test if the dataroot overrides below work.
+        c.update_default_dataset_config(app__about_legal_tos="tos_default.html")
+
+        # specialize the configs for set1
+        c.add_dataroot_config(
+            "s1", user_annotations__enable=False, diffexp__enable=True, app__about_legal_tos="tos_set1.html"
+        )
+
+        # specialize the configs for set2
+        c.add_dataroot_config(
+            "s2", user_annotations__enable=True, diffexp__enable=False, app__about_legal_tos="tos_set2.html"
+        )
+
+        # no specializations for set3 (they get the default dataset config)
         c.complete_config()
 
         with test_server(app_config=c) as server:
             session = requests.Session()
 
-            r = session.get(f"{server}/set1/pbmc3k.h5ad/api/v0.2/config")
+            r = session.get(f"{server}/set1/1/2/pbmc3k.h5ad/api/v0.2/config")
             data_config = r.json()
             assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
+            assert data_config["config"]["parameters"]["annotations"] is False
+            assert data_config["config"]["parameters"]["disable-diffexp"] is False
+            assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_set1.html"
 
             r = session.get(f"{server}/set2/pbmc3k.cxg/api/v0.2/config")
             data_config = r.json()
             assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
+            assert data_config["config"]["parameters"]["annotations"] is True
+            assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_set2.html"
+
+            r = session.get(f"{server}/set3/pbmc3k.cxg/api/v0.2/config")
+            data_config = r.json()
+            assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
+            assert data_config["config"]["parameters"]["annotations"] is True
+            assert data_config["config"]["parameters"]["disable-diffexp"] is False
+            assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_default.html"
 
             r = session.get(f"{server}/health")
             assert r.json()["status"] == "pass"

server/test/test_diffexp.py

@@ -15,8 +15,9 @@ class DiffExpTest(unittest.TestCase):
     """Tests the diffexp returns the expected results for one test case, using different
     adaptor types and different algorithms."""
 
-    def load_dataset(self, path, extra={}):
+    def load_dataset(self, path, extra_server_config={}, extra_dataset_config={}):
-        config = app_config(path, extra=extra)
+        config = app_config(path, extra_server_config=extra_server_config,
+                            extra_dataset_config=extra_dataset_config)
         loader = MatrixDataLoader(path)
         adaptor = loader.open(config)
         return adaptor
@@ -100,7 +101,7 @@ class DiffExpTest(unittest.TestCase):
             # create a sparse matrix
             h5adfile = os.path.join(dirname, "sparse.h5ad")
             create_test_h5ad(h5adfile, 2000, 2000, 10, apply_col_shift)
-            adaptor_anndata = self.load_dataset(h5adfile, extra=dict(embeddings__names=[]))
+            adaptor_anndata = self.load_dataset(h5adfile, extra_dataset_config=dict(embeddings__names=[]))
             adata = adaptor_anndata.data
 
             sparsename = os.path.join(dirname, "sparse.cxg")

server/test/test_eb.py

@@ -0,0 +1,54 @@
+import unittest
+import tempfile
+import requests
+import subprocess
+from server.test import PROJECT_ROOT
+from server.common.app_config import AppConfig
+from contextlib import contextmanager
+import time
+
+
+@contextmanager
+def run_eb_app(tempdirname):
+    ps = subprocess.Popen(["python", "artifact.dir/application.py"], cwd=tempdirname)
+    server = "http://localhost:5000"
+    for _ in range(10):
+        try:
+            requests.get(f"{server}/health")
+            break
+        except requests.exceptions.ConnectionError:
+            time.sleep(1)
+
+    try:
+        yield server
+    finally:
+        try:
+            ps.terminate()
+        except ProcessLookupError:
+            pass
+
+
+class Elastic_Beanstalk_Test(unittest.TestCase):
+    def test_run(self):
+
+        tempdir = tempfile.TemporaryDirectory(dir=f"{PROJECT_ROOT}/server")
+        tempdirname = tempdir.name
+
+        c = AppConfig()
+        # test that eb works
+        c.update_server_config(
+            multi_dataset__dataroot=f"{PROJECT_ROOT}/server/test/test_datasets", app__flask_secret_key="open sesame"
+        )
+
+        c.complete_config()
+        c.write_config(f"{tempdirname}/config.yaml")
+
+        subprocess.check_call(f"git ls-files . | cpio -pdm {tempdirname}", cwd=f"{PROJECT_ROOT}/server/eb", shell=True)
+        subprocess.check_call(["make", "build"], cwd=tempdirname)
+
+        with run_eb_app(tempdirname) as server:
+            session = requests.Session()
+
+            r = session.get(f"{server}/d/pbmc3k.cxg/api/v0.2/config")
+            data_config = r.json()
+            assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"

server/test/test_matrixcache.py

@@ -21,13 +21,13 @@ class MatrixCacheTest(unittest.TestCase):
             shutil.copytree(source, target)
 
     def use_dataset(self, matrix_cache, dirname, app_config, dataset_index):
-        with matrix_cache.data_adaptor(os.path.join(dirname, str(dataset_index) + ".cxg"), app_config) as adaptor:
+        with matrix_cache.data_adaptor(None, os.path.join(dirname, str(dataset_index) + ".cxg"), app_config) as adaptor:
             pass
         return adaptor
 
     def use_dataset_with_error(self, matrix_cache, dirname, app_config, dataset_index):
         try:
-            with matrix_cache.data_adaptor(os.path.join(dirname, str(dataset_index) + ".cxg"), app_config):
+            with matrix_cache.data_adaptor(None, os.path.join(dirname, str(dataset_index) + ".cxg"), app_config):
                 raise DatasetAccessError("something bad happened")
         except DatasetAccessError:
             # the MatrixDataCacheManager rethrows the exception, so catch and ignore
@@ -38,7 +38,7 @@ class MatrixCacheTest(unittest.TestCase):
         result = {}
         for k, v in datasets.items():
             # filter out the dirname and the .cxg from the name
-            newk = int(k[len(dirname) + 1 : -4])
+            newk = int(k[1][len(dirname) + 1 : -4])
             result[newk] = v
 
         return result

server/test/test_writable_annotation.py

@@ -15,12 +15,13 @@ from server.data_common.matrix_loader import MatrixDataType
 class WritableAnnotationTest(unittest.TestCase):
     def setUp(self):
         self.data, self.tmp_dir, self.annotations = data_with_tmp_annotations(MatrixDataType.H5AD)
+        self.data.dataset_config.user_annotations = self.annotations
 
     def tearDown(self):
         shutil.rmtree(self.tmp_dir)
 
     def annotation_put_fbs(self, fbs):
-        annotations_put_fbs_helper(self.data, self.annotations, fbs)
+        annotations_put_fbs_helper(self.data, fbs)
         res = json.dumps({"status": "OK"})
         return res
 
@@ -112,7 +113,7 @@ class WritableAnnotationTest(unittest.TestCase):
         # get
         labels = self.annotations.read_labels(None)
         fbsAll = self.data.annotation_to_fbs_matrix("obs", None, labels)
-        schema = schema_get_helper(self.data, self.annotations)
+        schema = schema_get_helper(self.data)
         annotations = decode_fbs.decode_matrix_FBS(fbsAll)
         obs_index_col_name = schema["annotations"]["obs"]["index"]
         self.assertEqual(annotations["n_rows"], n_rows)
@@ -149,7 +150,7 @@ class WritableAnnotationTest(unittest.TestCase):
             self.assertEqual(len(feature), 1)
 
         check_feature("POST", "/cluster/", False)
-        check_feature("POST", "/diffexp/", self.data.config.diffexp__enable)
+        check_feature("POST", "/diffexp/", self.data.dataset_config.diffexp__enable)
         check_feature("GET", "/layout/obs", True)
-        check_feature("PUT", "/layout/obs", self.data.config.embeddings__enable_reembedding)
+        check_feature("PUT", "/layout/obs", self.data.dataset_config.embeddings__enable_reembedding)
         check_feature("PUT", "/annotations/obs", True)