mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-02 22:48:12 +08:00
Refactor czi_hosted and server into backend directory, pull common code into backend/common, refactor tests (#2102)
* move local_server -> backend/server server-> backend/czi_hosted, pull common code into backend/common update imports, tests and make commands
This commit is contained in:
Madison Dunitz
@@ -0,0 +1,4 @@
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from backend.common.utils.aws_secret_utils import get_secret_key # noqa F504
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DEFAULT_SERVER_PORT = 5005
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BIG_FILE_SIZE_THRESHOLD = 100 * 2 ** 20 # 100MB
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@@ -0,0 +1,171 @@
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import yaml
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from flatten_dict import unflatten
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from backend.server.default_config import get_default_config
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from backend.server.common.config.dataset_config import DatasetConfig
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from backend.server.common.config.server_config import ServerConfig
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from backend.server.common.config.external_config import ExternalConfig
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from backend.common.errors import ConfigurationError
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class AppConfig(object):
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"""
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AppConfig stores all the configuration for cellxgene.
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AppConfig contains one or more DatasetConfig(s) and one ServerConfig.
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The server_config contains attributes that refer to the server process as a whole.
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The dataset_config refers to attributes that are associated with the features and
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presentations of a dataset.
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AppConfig has methods to initialize, modify, and access the configuration.
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"""
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def __init__(self):
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# the default configuration (see default_config.py)
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# TODO @madison -- if we always read from the default config (hard coded path) can we set those values as
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# defaults within the config class?
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self.default_config = get_default_config()
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# the server configuration
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self.server_config = ServerConfig(self, self.default_config["server"])
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# the dataset config
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self.dataset_config = DatasetConfig(None, self, self.default_config["dataset"])
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# external config
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self.external_config = ExternalConfig(self, self.default_config["external"])
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# Set to true when config_completed is called
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self.is_completed = False
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def get_dataset_config(self):
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return self.dataset_config
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def check_config(self):
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"""Verify all the attributes in the config have been type checked"""
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if not self.is_completed:
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raise ConfigurationError("The configuration has not been completed")
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self.server_config.check_config()
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self.dataset_config.check_config()
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self.external_config.check_config()
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def update_server_config(self, **kw):
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self.server_config.update(**kw)
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self.is_complete = False
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def update_dataset_config(self, **kw):
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self.dataset_config.update(**kw)
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self.is_complete = False
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def update_single_config_from_path_and_value(self, path, value):
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"""Update a single config parameter with the value.
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Path is a list of string, that gives a path to the config parameter to be updated.
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For example, path may be ["server","app","port"].
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"""
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self.is_complete = False
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if not isinstance(path, list):
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raise ConfigurationError(f"path must be a list of strings, got '{str(path)}'")
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for part in path:
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if not isinstance(part, str):
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raise ConfigurationError(f"path must be a list of strings, got '{str(path)}'")
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if len(path) < 1 or path[0] not in ("server", "dataset"):
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raise ConfigurationError("path must start with 'server', or 'dataset'")
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if path[0] == "server":
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attr = "__".join(path[1:])
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try:
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self.update_server_config(**{attr: value})
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except ConfigurationError:
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raise ConfigurationError(f"unknown config parameter at path: '{str(path)}'")
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elif path[0] == "dataset":
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attr = "__".join(path[1:])
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try:
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self.update_dataset_config(**{attr: value})
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except ConfigurationError:
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raise ConfigurationError(f"unknown config parameter at path: '{str(path)}'")
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def update_from_config_file(self, config_file):
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try:
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with open(config_file) as yml_file:
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config = yaml.safe_load(yml_file)
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except yaml.YAMLError as e:
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raise ConfigurationError(f"The specified config file contained an error: {e}")
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except OSError as e:
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raise ConfigurationError(f"Issue retrieving the specified config file: {e}")
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if config.get("server"):
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self.server_config.update_from_config(config["server"], "server")
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if config.get("dataset"):
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self.dataset_config.update_from_config(config["dataset"], "dataset")
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if config.get("external"):
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self.external_config.update_from_config(config["external"], "external")
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self.is_complete = False
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def config_to_dict(self):
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"""return the configuration as an unflattened dict"""
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server = self.server_config.create_mapping(self.server_config.default_config)
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dataset = self.dataset_config.create_mapping(self.dataset_config.default_config)
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external = self.external_config.create_mapping(self.external_config.default_config)
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config = dict(server={}, dataset={})
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for attrname in server.keys():
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config["server__" + attrname] = getattr(self.server_config, attrname)
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for attrname in dataset.keys():
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config["dataset__" + attrname] = getattr(self.dataset_config, attrname)
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for attrname in external.keys():
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config["external__" + attrname] = getattr(self.external_config, attrname)
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config = unflatten(config, splitter=lambda key: key.split("__"))
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return config
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def write_config(self, config_file):
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"""output the config to a yaml file"""
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config = self.config_to_dict()
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yaml.dump(config, open(config_file, "w"))
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def changes_from_default(self):
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"""Return all the attribute that are different from the default"""
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diff_server = self.server_config.changes_from_default()
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diff_dataset = self.dataset_config.changes_from_default()
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diff_external = self.external.changes_from_default()
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diff = dict(server=diff_server, dataset=diff_dataset, external=diff_external)
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return diff
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def complete_config(self, messagefn=None):
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"""The configure options are checked, and any additional setup based on the config
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parameters is done"""
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if messagefn is None:
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def noop(message):
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pass
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messagefn = noop
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# TODO: to give better error messages we can add a mapping between where each config
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# attribute originated (e.g. command line argument or config file), then in the error
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# messages we can give correct context for attributes with bad value.
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context = dict(messagefn=messagefn)
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# complete config for external_config first, since this may update values in the other sections
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self.external_config.complete_config(context)
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self.server_config.complete_config(context)
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self.dataset_config.complete_config(context)
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self.is_completed = True
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self.check_config()
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def get_matrix_data_cache_manager(self):
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return self.server_config.matrix_data_cache_manager
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def get_title(self, data_adaptor):
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return (
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self.server_config.single_dataset__title
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if self.server_config.single_dataset__title
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else data_adaptor.get_title()
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)
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def get_about(self, data_adaptor):
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return (
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self.server_config.single_dataset__about
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if self.server_config.single_dataset__about
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else data_adaptor.get_about()
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)
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@@ -0,0 +1,99 @@
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import copy
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from flatten_dict import flatten
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from backend.common.errors import ConfigurationError
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class BaseConfig(object):
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"""
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This class handles the mechanics of updating and checking attributes.
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Derived classes are expected to store the actual attributes
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Currently DatasetConfig and ServerConfig both inherit from BaseConfig.
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"""
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def __init__(self, app_config, default_config):
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# reference back to the app_config
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self.app_config = app_config
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# the complete set of attributes and their default values (unflattened)
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self.default_config = default_config
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# used to make sure every attribute value is checked
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self.attr_checked = {key_name: False for key_name in self.create_mapping(default_config).keys()}
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def create_mapping(self, config):
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"""
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Create a dictionary where the keys are the name of attributes (using double underscore convention)
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For example: authentication__type
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The values are a tuple,
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- the first item of the tuple is a tuple of path elements (location in config 'tree')
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- the second item is the value of the config parameter
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For example: (('authentication', 'type'), 'session'))
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"""
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config_copy = copy.deepcopy(config)
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mapping = {}
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flat_config = flatten(config_copy)
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for key, value in flat_config.items():
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# name of the attribute
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attr = "__".join(key)
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mapping[attr] = (key, value)
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return mapping
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def validate_correct_type_of_configuration_attribute(self, attrname, vtype):
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val = getattr(self, attrname)
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if type(vtype) in (list, tuple):
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if type(val) not in vtype:
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tnames = ",".join([x.__name__ for x in vtype])
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raise ConfigurationError(
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f"Invalid type for attribute: {attrname}, expected types ({tnames}), got {type(val).__name__}"
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)
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else:
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if type(val) != vtype:
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raise ConfigurationError(
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f"Invalid type for attribute: {attrname}, "
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f"expected type {vtype.__name__}, got {type(val).__name__}"
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)
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self.attr_checked[attrname] = True
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def check_config(self):
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mapping = self.create_mapping(self.default_config)
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for key in mapping.keys():
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if not self.attr_checked[key]:
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raise ConfigurationError(f"The attr '{key}' has not been checked")
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def update(self, **kw):
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"""Update the attributes defined in kw with their new values."""
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for key, value in kw.items():
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if not hasattr(self, key):
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raise ConfigurationError(f"unknown config parameter {key}.")
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try:
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if type(value) == tuple:
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# convert tuple values to list values
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value = list(value)
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setattr(self, key, value)
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except KeyError:
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raise ConfigurationError(f"Unable to set config parameter {key}.")
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self.attr_checked[key] = False
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def update_from_config(self, config, prefix):
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mapping = self.create_mapping(config)
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for attr, (key, value) in mapping.items():
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if not hasattr(self, attr):
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raise ConfigurationError(f"Unknown key from config file: {prefix}__{attr}")
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setattr(self, attr, value)
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self.attr_checked[attr] = False
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def changes_from_default(self):
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"""Return all the attribute that are different from the default"""
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mapping = self.create_mapping(self.default_config)
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diff = []
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for attrname, (key, defval) in mapping.items():
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curval = getattr(self, attrname)
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if curval != defval:
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diff.append((attrname, curval, defval))
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return diff
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@@ -0,0 +1,123 @@
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from backend.server import display_version as cellxgene_display_version
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def get_client_config(app_config, data_adaptor):
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"""
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Return the configuration as required by the /config REST route
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"""
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server_config = app_config.server_config
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dataset_config = data_adaptor.dataset_config
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annotation = dataset_config.user_annotations
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auth = server_config.auth
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# FIXME The current set of config is not consistently presented:
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# we have camalCase, hyphen-text, and underscore_text
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# make sure the configuration has been checked.
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app_config.check_config()
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# display_names
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title = app_config.get_title(data_adaptor)
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about = app_config.get_about(data_adaptor)
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display_names = dict(engine=data_adaptor.get_name(), dataset=title)
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# library_versions
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library_versions = {}
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library_versions.update(data_adaptor.get_library_versions())
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library_versions["cellxgene"] = cellxgene_display_version
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# links
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links = {"about-dataset": about}
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# parameters
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parameters = {
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"layout": dataset_config.embeddings__names,
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"max-category-items": dataset_config.presentation__max_categories,
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"obs_names": server_config.single_dataset__obs_names,
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"var_names": server_config.single_dataset__var_names,
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"diffexp_lfc_cutoff": dataset_config.diffexp__lfc_cutoff,
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"backed": server_config.adaptor__anndata_adaptor__backed,
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"disable-diffexp": not dataset_config.diffexp__enable,
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"enable-reembedding": dataset_config.embeddings__enable_reembedding,
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"annotations": False,
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"annotations_file": None,
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"annotations_dir": None,
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"annotations_genesets": True, # feature flag
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"annotations_genesets_readonly": dataset_config.user_annotations__gene_sets__readonly,
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"annotations_genesets_summary_methods": ["mean"],
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"annotations_cell_ontology_enabled": False,
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"annotations_cell_ontology_obopath": None,
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"annotations_cell_ontology_terms": None,
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"custom_colors": dataset_config.presentation__custom_colors,
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"diffexp-may-be-slow": False,
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}
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# corpora dataset_props
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# TODO/Note: putting info from the dataset into the /config is not ideal.
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# However, it is definitely not part of /schema, and we do not have a top-level
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# route for data properties. Consider creating one at some point.
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corpora_props = data_adaptor.get_corpora_props()
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if corpora_props and "default_embedding" in corpora_props:
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default_embedding = corpora_props["default_embedding"]
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if isinstance(default_embedding, str) and default_embedding.startswith("X_"):
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default_embedding = default_embedding[2:] # drop X_ prefix
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if default_embedding in data_adaptor.get_embedding_names():
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parameters["default_embedding"] = default_embedding
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data_adaptor.update_parameters(parameters)
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if annotation:
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annotation.update_parameters(parameters, data_adaptor)
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# gather it all together
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client_config = {}
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config = client_config["config"] = {}
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config["displayNames"] = display_names
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config["library_versions"] = library_versions
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config["links"] = links
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config["parameters"] = parameters
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config["corpora_props"] = corpora_props
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config["limits"] = {
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"column_request_max": server_config.limits__column_request_max,
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"diffexp_cellcount_max": server_config.limits__diffexp_cellcount_max,
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}
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if dataset_config.app__authentication_enable and auth.is_valid_authentication_type():
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config["authentication"] = {
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"requires_client_login": auth.requires_client_login(),
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}
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if auth.requires_client_login():
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config["authentication"].update(
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{
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# Todo why are these stored on the data_adaptor?
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"login": auth.get_login_url(data_adaptor),
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"logout": auth.get_logout_url(data_adaptor),
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}
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)
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return client_config
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def get_client_userinfo(app_config, data_adaptor):
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"""
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Return the userinfo as required by the /userinfo REST route
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"""
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server_config = app_config.server_config
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dataset_config = data_adaptor.dataset_config
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auth = server_config.auth
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# make sure the configuration has been checked.
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app_config.check_config()
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if dataset_config.app__authentication_enable and auth.is_valid_authentication_type():
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userinfo = {}
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userinfo["userinfo"] = {
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"is_authenticated": auth.is_user_authenticated(),
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"username": auth.get_user_name(),
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"user_id": auth.get_user_id(),
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"email": auth.get_user_email(),
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"picture": auth.get_user_picture(),
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}
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return userinfo
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@@ -0,0 +1,222 @@
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import os
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from os.path import splitext, isdir
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from backend.server.common.annotations.local_file_csv import AnnotationsLocalFile
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from backend.server.common.config.base_config import BaseConfig
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from backend.common.errors import ConfigurationError, OntologyLoadFailure, AnnotationsError
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from backend.server.compute.scanpy import get_scanpy_module
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from backend.server.data_common.matrix_loader import MatrixDataLoader
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class DatasetConfig(BaseConfig):
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"""Manages the config attribute associated with a dataset."""
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def __init__(self, tag, app_config, default_config):
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super().__init__(app_config, default_config)
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self.tag = tag
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try:
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self.app__scripts = default_config["app"]["scripts"]
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self.app__inline_scripts = default_config["app"]["inline_scripts"]
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self.app__authentication_enable = default_config["app"]["authentication_enable"]
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self.presentation__max_categories = default_config["presentation"]["max_categories"]
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self.presentation__custom_colors = default_config["presentation"]["custom_colors"]
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self.user_annotations__enable = default_config["user_annotations"]["enable"]
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self.user_annotations__type = default_config["user_annotations"]["type"]
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self.user_annotations__local_file_csv__directory = default_config["user_annotations"]["local_file_csv"][
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"directory"
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]
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self.user_annotations__local_file_csv__file = default_config["user_annotations"]["local_file_csv"]["file"]
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self.user_annotations__ontology__enable = default_config["user_annotations"]["ontology"]["enable"]
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self.user_annotations__ontology__obo_location = default_config["user_annotations"]["ontology"][
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"obo_location"
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]
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self.user_annotations__gene_sets__readonly = default_config["user_annotations"]["gene_sets"]["readonly"]
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self.user_annotations__local_file_csv__gene_sets_file = default_config["user_annotations"][
|
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"local_file_csv"
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]["gene_sets_file"]
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self.embeddings__names = default_config["embeddings"]["names"]
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self.embeddings__enable_reembedding = default_config["embeddings"]["enable_reembedding"]
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self.diffexp__enable = default_config["diffexp"]["enable"]
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self.diffexp__lfc_cutoff = default_config["diffexp"]["lfc_cutoff"]
|
||||
self.diffexp__top_n = default_config["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()
|
||||
self.handle_presentation()
|
||||
self.handle_user_annotations(context)
|
||||
self.handle_embeddings()
|
||||
self.handle_diffexp(context)
|
||||
|
||||
def get_data_adaptor(self):
|
||||
server_config = self.app_config.server_config
|
||||
if not server_config.data_adaptor:
|
||||
matrix_data_loader = MatrixDataLoader(server_config.single_dataset__datapath, app_config=self.app_config)
|
||||
server_config.data_adaptor = matrix_data_loader.open(self.app_config)
|
||||
|
||||
return server_config.data_adaptor
|
||||
|
||||
def handle_app(self):
|
||||
self.validate_correct_type_of_configuration_attribute("app__scripts", list)
|
||||
self.validate_correct_type_of_configuration_attribute("app__inline_scripts", list)
|
||||
self.validate_correct_type_of_configuration_attribute("app__authentication_enable", bool)
|
||||
|
||||
# scripts can be string (filename) or dict (attributes). Convert string to dict.
|
||||
scripts = []
|
||||
for script in self.app__scripts:
|
||||
try:
|
||||
if isinstance(script, str):
|
||||
scripts.append({"src": script})
|
||||
elif isinstance(script, dict) and isinstance(script["src"], str):
|
||||
scripts.append(script)
|
||||
else:
|
||||
raise Exception
|
||||
except Exception as e:
|
||||
raise ConfigurationError(f"Scripts must be string or a dict containing an src key: {e}")
|
||||
|
||||
self.app__scripts = scripts
|
||||
|
||||
def handle_presentation(self):
|
||||
self.validate_correct_type_of_configuration_attribute("presentation__max_categories", int)
|
||||
self.validate_correct_type_of_configuration_attribute("presentation__custom_colors", bool)
|
||||
|
||||
def handle_user_annotations(self, context):
|
||||
self.validate_correct_type_of_configuration_attribute("user_annotations__enable", bool)
|
||||
self.validate_correct_type_of_configuration_attribute("user_annotations__type", str)
|
||||
self.validate_correct_type_of_configuration_attribute(
|
||||
"user_annotations__local_file_csv__directory", (type(None), str)
|
||||
)
|
||||
self.validate_correct_type_of_configuration_attribute(
|
||||
"user_annotations__local_file_csv__file", (type(None), str)
|
||||
)
|
||||
self.validate_correct_type_of_configuration_attribute(
|
||||
"user_annotations__local_file_csv__gene_sets_file", (type(None), str)
|
||||
)
|
||||
self.validate_correct_type_of_configuration_attribute("user_annotations__ontology__enable", bool)
|
||||
self.validate_correct_type_of_configuration_attribute(
|
||||
"user_annotations__ontology__obo_location", (type(None), str)
|
||||
)
|
||||
self.validate_correct_type_of_configuration_attribute("user_annotations__gene_sets__readonly", bool)
|
||||
|
||||
if self.user_annotations__enable or not self.user_annotations__gene_sets__readonly:
|
||||
server_config = self.app_config.server_config
|
||||
if not self.app__authentication_enable:
|
||||
raise ConfigurationError("user annotations requires authentication to be enabled")
|
||||
if not server_config.auth.is_valid_authentication_type():
|
||||
auth_type = server_config.authentication__type
|
||||
raise ConfigurationError(f"authentication method {auth_type} is not compatible with user annotations")
|
||||
|
||||
# Must always have an annotations instance to support genesets. User annotation (cell labels) are optional
|
||||
# as are writable gene sets
|
||||
if self.user_annotations__type == "local_file_csv":
|
||||
self.handle_local_file_csv_annotations(context)
|
||||
else:
|
||||
raise ConfigurationError('The only annotation type support is "local_file_csv"')
|
||||
|
||||
if self.user_annotations__enable:
|
||||
if self.user_annotations__ontology__enable or self.user_annotations__ontology__obo_location:
|
||||
try:
|
||||
self.user_annotations.load_ontology(self.user_annotations__ontology__obo_location)
|
||||
except OntologyLoadFailure as e:
|
||||
raise ConfigurationError("Unable to load ontology terms\n" + str(e))
|
||||
|
||||
self.check_annotation_config_vars_not_set(context)
|
||||
|
||||
def handle_local_file_csv_annotations(self, context):
|
||||
dirname = self.user_annotations__local_file_csv__directory
|
||||
filename = self.user_annotations__local_file_csv__file
|
||||
genesets_filename = self.user_annotations__local_file_csv__gene_sets_file
|
||||
|
||||
if dirname is not None and (filename is not None or genesets_filename is not None):
|
||||
raise ConfigurationError(
|
||||
"'user-generated-data-dir' may not be used with annotations-file' or 'genesets-file'."
|
||||
)
|
||||
|
||||
if filename is not None:
|
||||
lf_name, lf_ext = splitext(filename)
|
||||
if lf_ext and lf_ext != ".csv":
|
||||
raise ConfigurationError(f"annotation file type must be .csv: {filename}")
|
||||
|
||||
if genesets_filename is not None:
|
||||
lf_name, lf_ext = splitext(genesets_filename)
|
||||
if lf_ext and lf_ext != ".csv":
|
||||
raise ConfigurationError(f"genesets file type must be .csv: {genesets_filename}")
|
||||
|
||||
if dirname is not None and not isdir(dirname):
|
||||
try:
|
||||
os.mkdir(dirname)
|
||||
except OSError:
|
||||
raise ConfigurationError("Unable to create directory specified by --user-generated-data-dir")
|
||||
|
||||
anno_config = {
|
||||
"user-annotations": self.user_annotations__enable,
|
||||
"genesets-save": not self.user_annotations__gene_sets__readonly,
|
||||
}
|
||||
self.user_annotations = AnnotationsLocalFile(anno_config, dirname, filename, genesets_filename)
|
||||
|
||||
# if the user has specified a fixed label file, go ahead and validate it
|
||||
# so that we can remove errors early in the process.
|
||||
server_config = self.app_config.server_config
|
||||
if server_config.single_dataset__datapath:
|
||||
data_adaptor = self.get_data_adaptor()
|
||||
if self.user_annotations__local_file_csv__file:
|
||||
self.user_annotations.read_labels(data_adaptor)
|
||||
if self.user_annotations__local_file_csv__gene_sets_file:
|
||||
try:
|
||||
self.user_annotations.read_gene_sets(data_adaptor, context)
|
||||
except (ValueError, AnnotationsError, KeyError) as e:
|
||||
raise ConfigurationError(f"Unable to read genesets CSV file: {str(e)}") from e
|
||||
|
||||
def check_annotation_config_vars_not_set(self, context):
|
||||
if self.user_annotations__type is not None:
|
||||
dirname = self.user_annotations__local_file_csv__directory
|
||||
filename = self.user_annotations__local_file_csv__file
|
||||
if not self.user_annotations__enable:
|
||||
if filename is not None:
|
||||
context["messagefn"]("Warning: --annotations-file ignored as annotations are disabled.")
|
||||
if self.user_annotations__ontology__enable:
|
||||
context["messagefn"](
|
||||
"Warning: --experimental-annotations-ontology ignored as annotations are disabled."
|
||||
)
|
||||
if self.user_annotations__ontology__obo_location is not None:
|
||||
context["messagefn"](
|
||||
"Warning: --experimental-annotations-ontology-obo ignored as annotations are disabled."
|
||||
)
|
||||
if dirname is not None:
|
||||
context["messagefn"]("Warning: --user-generated-data-dir ignored as annotations are disabled.")
|
||||
|
||||
def handle_embeddings(self):
|
||||
self.validate_correct_type_of_configuration_attribute("embeddings__names", list)
|
||||
self.validate_correct_type_of_configuration_attribute("embeddings__enable_reembedding", bool)
|
||||
|
||||
server_config = self.app_config.server_config
|
||||
if self.embeddings__enable_reembedding:
|
||||
if server_config.single_dataset__datapath:
|
||||
if server_config.adaptor__anndata_adaptor__backed:
|
||||
raise ConfigurationError("enable-reembedding is not supported when run in --backed mode.")
|
||||
|
||||
try:
|
||||
get_scanpy_module()
|
||||
except NotImplementedError:
|
||||
# Todo add scanpy to requirements.txt and remove this check once re-embeddings is fully supported
|
||||
raise ConfigurationError("Please install scanpy to enable UMAP re-embedding")
|
||||
|
||||
def handle_diffexp(self, context):
|
||||
self.validate_correct_type_of_configuration_attribute("diffexp__enable", bool)
|
||||
self.validate_correct_type_of_configuration_attribute("diffexp__lfc_cutoff", float)
|
||||
self.validate_correct_type_of_configuration_attribute("diffexp__top_n", int)
|
||||
|
||||
data_adaptor = self.get_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."
|
||||
)
|
||||
@@ -0,0 +1,96 @@
|
||||
import os
|
||||
|
||||
from backend.server.common.config.base_config import BaseConfig
|
||||
from backend.common.errors import ConfigurationError
|
||||
from backend.server.common.config import get_secret_key
|
||||
from backend.common.errors import SecretKeyRetrievalError
|
||||
from backend.common.utils.type_conversion_utils import convert_string_to_value
|
||||
|
||||
|
||||
class ExternalConfig(BaseConfig):
|
||||
"""Manages the config attribute associated with external configuration sources, such as
|
||||
environment variables or the AWS Secrets Manager."""
|
||||
|
||||
def __init__(self, app_config, default_config):
|
||||
super().__init__(app_config, default_config)
|
||||
try:
|
||||
self.environment = default_config["environment"]
|
||||
self.aws_secrets_manager__region = default_config["aws_secrets_manager"]["region"]
|
||||
self.aws_secrets_manager__secrets = default_config["aws_secrets_manager"]["secrets"]
|
||||
|
||||
except KeyError as e:
|
||||
raise ConfigurationError(f"Unexpected config: {str(e)}")
|
||||
|
||||
def complete_config(self, context):
|
||||
self.handle_environment(context)
|
||||
self.handle_aws_secrets_manager(context)
|
||||
|
||||
def handle_environment(self, context):
|
||||
"""For each environment variable defined, get the value (if it is set),
|
||||
and set the specified config parameter"""
|
||||
self.validate_correct_type_of_configuration_attribute("environment", list)
|
||||
for envdict in self.environment:
|
||||
name = envdict.get("name")
|
||||
if name is None:
|
||||
raise ConfigurationError("environment: 'name' is missing")
|
||||
required = envdict.get("required", False)
|
||||
if type(required) != bool:
|
||||
raise ConfigurationError("environment: 'required' must be a bool")
|
||||
path = envdict.get("path")
|
||||
if path is None:
|
||||
raise ConfigurationError("environment: 'path' is missing")
|
||||
|
||||
value = os.environ.get(name)
|
||||
if value is None:
|
||||
if required:
|
||||
raise ConfigurationError(f"required environment variable '{name}' not set")
|
||||
else:
|
||||
value = convert_string_to_value(value)
|
||||
self.app_config.update_single_config_from_path_and_value(path, value)
|
||||
|
||||
def handle_aws_secrets_manager(self, context):
|
||||
"""For each aws secret defined, get the key/values, and set the specified config parameter"""
|
||||
self.validate_correct_type_of_configuration_attribute("aws_secrets_manager__region", (type(None), str))
|
||||
self.validate_correct_type_of_configuration_attribute("aws_secrets_manager__secrets", list)
|
||||
|
||||
if not self.aws_secrets_manager__secrets:
|
||||
return
|
||||
|
||||
self.validate_correct_type_of_configuration_attribute("aws_secrets_manager__region", str)
|
||||
|
||||
for secret in self.aws_secrets_manager__secrets:
|
||||
secret_name = secret.get("name")
|
||||
if secret_name is None:
|
||||
raise ConfigurationError("aws_secrets_manager: 'name' is missing")
|
||||
if not isinstance(secret_name, str):
|
||||
raise ConfigurationError("aws_secrets_manager: 'name' must be a string")
|
||||
|
||||
try:
|
||||
secret_dict = get_secret_key(self.aws_secrets_manager__region, secret_name)
|
||||
except SecretKeyRetrievalError as e:
|
||||
raise ConfigurationError(f"Unable to retrieve secret {secret_name}: {str(e)}")
|
||||
|
||||
values = secret.get("values")
|
||||
if values is None:
|
||||
raise ConfigurationError("aws_secrets_manager: 'values' is missing")
|
||||
if not isinstance(values, list):
|
||||
raise ConfigurationError("aws_secrets_manager: 'values' must be a list")
|
||||
|
||||
for value in values:
|
||||
key = value.get("key")
|
||||
if key is None:
|
||||
raise ConfigurationError(f"missing 'key' in secret values: {secret_name}")
|
||||
path = value.get("path")
|
||||
if path is None:
|
||||
raise ConfigurationError(f"missing 'path' in secret values: {secret_name}")
|
||||
required = value.get("required", False)
|
||||
if type(required) != bool:
|
||||
raise ConfigurationError(f"wrong type for 'required' in secret values: {secret_name}")
|
||||
|
||||
secret_value = secret_dict.get(key)
|
||||
if secret_value is None:
|
||||
if required:
|
||||
raise ConfigurationError(f"required secret '{secret_name}:{key}' not set")
|
||||
else:
|
||||
secret_value = convert_string_to_value(secret_value)
|
||||
self.app_config.update_single_config_from_path_and_value(path, secret_value)
|
||||
@@ -0,0 +1,183 @@
|
||||
import os
|
||||
import sys
|
||||
import warnings
|
||||
from os.path import basename
|
||||
from urllib.parse import urlparse
|
||||
|
||||
from backend.server.auth.auth import AuthTypeFactory
|
||||
from backend.server.common.config.base_config import BaseConfig
|
||||
from backend.server.common.config import DEFAULT_SERVER_PORT, BIG_FILE_SIZE_THRESHOLD
|
||||
from backend.common.utils.data_locator import discover_s3_region_name
|
||||
from backend.common.errors import ConfigurationError, DatasetAccessError
|
||||
from backend.common.utils.utils import is_port_available, find_available_port, custom_format_warning
|
||||
from backend.server.data_common.matrix_loader import MatrixDataLoader
|
||||
|
||||
|
||||
class ServerConfig(BaseConfig):
|
||||
"""Manages the config attribute associated with the server."""
|
||||
|
||||
def __init__(self, app_config, default_config):
|
||||
super().__init__(app_config, default_config)
|
||||
|
||||
try:
|
||||
self.app__verbose = default_config["app"]["verbose"]
|
||||
self.app__debug = default_config["app"]["debug"]
|
||||
self.app__host = default_config["app"]["host"]
|
||||
self.app__port = default_config["app"]["port"]
|
||||
self.app__open_browser = default_config["app"]["open_browser"]
|
||||
self.app__force_https = default_config["app"]["force_https"]
|
||||
self.app__flask_secret_key = default_config["app"]["flask_secret_key"]
|
||||
|
||||
self.authentication__type = default_config["authentication"]["type"]
|
||||
self.authentication__insecure_test_environment = default_config["authentication"][
|
||||
"insecure_test_environment"
|
||||
]
|
||||
|
||||
self.single_dataset__datapath = default_config["single_dataset"]["datapath"]
|
||||
self.single_dataset__obs_names = default_config["single_dataset"]["obs_names"]
|
||||
self.single_dataset__var_names = default_config["single_dataset"]["var_names"]
|
||||
self.single_dataset__about = default_config["single_dataset"]["about"]
|
||||
self.single_dataset__title = default_config["single_dataset"]["title"]
|
||||
|
||||
self.data_locator__s3__region_name = default_config["data_locator"]["s3"]["region_name"]
|
||||
|
||||
self.adaptor__anndata_adaptor__backed = default_config["adaptor"]["anndata_adaptor"]["backed"]
|
||||
|
||||
self.limits__diffexp_cellcount_max = default_config["limits"]["diffexp_cellcount_max"]
|
||||
self.limits__column_request_max = default_config["limits"]["column_request_max"]
|
||||
|
||||
except KeyError as e:
|
||||
raise ConfigurationError(f"Unexpected config: {str(e)}")
|
||||
|
||||
self.data_adaptor = None
|
||||
|
||||
# The authentication object
|
||||
self.auth = None
|
||||
|
||||
def complete_config(self, context):
|
||||
self.handle_app(context)
|
||||
self.handle_data_source()
|
||||
self.handle_authentication()
|
||||
self.handle_data_locator()
|
||||
self.handle_adaptor() # may depend on data_locator
|
||||
self.handle_single_dataset(context) # may depend on adaptor
|
||||
self.handle_limits()
|
||||
|
||||
self.check_config()
|
||||
|
||||
def handle_app(self, context):
|
||||
self.validate_correct_type_of_configuration_attribute("app__verbose", bool)
|
||||
self.validate_correct_type_of_configuration_attribute("app__debug", bool)
|
||||
self.validate_correct_type_of_configuration_attribute("app__host", str)
|
||||
self.validate_correct_type_of_configuration_attribute("app__port", (type(None), int))
|
||||
self.validate_correct_type_of_configuration_attribute("app__open_browser", bool)
|
||||
self.validate_correct_type_of_configuration_attribute("app__force_https", bool)
|
||||
self.validate_correct_type_of_configuration_attribute("app__flask_secret_key", str)
|
||||
|
||||
if self.app__port:
|
||||
try:
|
||||
if not is_port_available(self.app__host, self.app__port):
|
||||
raise ConfigurationError(
|
||||
f"The port selected {self.app__port} is in use, please configure an open port."
|
||||
)
|
||||
except OverflowError:
|
||||
raise ConfigurationError(f"Invalid port: {self.app__port}")
|
||||
else:
|
||||
try:
|
||||
default_server_port = int(os.environ.get("CXG_SERVER_PORT", DEFAULT_SERVER_PORT))
|
||||
except ValueError:
|
||||
raise ConfigurationError(
|
||||
"Invalid port from environment variable CXG_SERVER_PORT: " + os.environ.get("CXG_SERVER_PORT")
|
||||
)
|
||||
try:
|
||||
self.app__port = find_available_port(self.app__host, default_server_port)
|
||||
except OverflowError:
|
||||
raise ConfigurationError(f"Invalid port: {default_server_port}")
|
||||
|
||||
if self.app__debug:
|
||||
context["messagefn"]("in debug mode, setting verbose=True and open_browser=False")
|
||||
self.app__verbose = True
|
||||
self.app__open_browser = False
|
||||
else:
|
||||
warnings.formatwarning = custom_format_warning
|
||||
|
||||
if not self.app__verbose:
|
||||
sys.tracebacklimit = 0
|
||||
|
||||
def handle_authentication(self):
|
||||
self.validate_correct_type_of_configuration_attribute("authentication__type", (type(None), str))
|
||||
self.validate_correct_type_of_configuration_attribute("authentication__insecure_test_environment", bool)
|
||||
|
||||
if self.authentication__type == "test" and not self.authentication__insecure_test_environment:
|
||||
raise ConfigurationError("Test auth can only be used in an insecure test environment")
|
||||
|
||||
self.auth = AuthTypeFactory.create(self.authentication__type, self)
|
||||
if self.auth is None:
|
||||
raise ConfigurationError(f"Unknown authentication type: {self.authentication__type}")
|
||||
|
||||
def handle_data_locator(self):
|
||||
self.validate_correct_type_of_configuration_attribute("data_locator__s3__region_name", (type(None), bool, str))
|
||||
if self.data_locator__s3__region_name is True:
|
||||
path = self.single_dataset__datapath
|
||||
|
||||
if path.startswith("s3://"):
|
||||
region_name = discover_s3_region_name(path)
|
||||
if region_name is None:
|
||||
raise ConfigurationError(f"Unable to discover s3 region name from {path}")
|
||||
else:
|
||||
region_name = None
|
||||
self.data_locator__s3__region_name = region_name
|
||||
|
||||
def handle_data_source(self):
|
||||
self.validate_correct_type_of_configuration_attribute("single_dataset__datapath", str)
|
||||
|
||||
def handle_single_dataset(self, context):
|
||||
self.validate_correct_type_of_configuration_attribute("single_dataset__datapath", (str, type(None)))
|
||||
self.validate_correct_type_of_configuration_attribute("single_dataset__title", (str, type(None)))
|
||||
self.validate_correct_type_of_configuration_attribute("single_dataset__about", (str, type(None)))
|
||||
self.validate_correct_type_of_configuration_attribute("single_dataset__obs_names", (str, type(None)))
|
||||
self.validate_correct_type_of_configuration_attribute("single_dataset__var_names", (str, type(None)))
|
||||
|
||||
# preload this data set
|
||||
matrix_data_loader = MatrixDataLoader(self.single_dataset__datapath, app_config=self.app_config)
|
||||
try:
|
||||
matrix_data_loader.pre_load_validation()
|
||||
except DatasetAccessError as e:
|
||||
raise ConfigurationError(str(e))
|
||||
|
||||
file_size = matrix_data_loader.file_size()
|
||||
file_basename = basename(self.single_dataset__datapath)
|
||||
if file_size > BIG_FILE_SIZE_THRESHOLD:
|
||||
context["messagefn"](f"Loading data from {file_basename}, this may take a while...")
|
||||
else:
|
||||
context["messagefn"](f"Loading data from {file_basename}.")
|
||||
|
||||
if self.single_dataset__about:
|
||||
|
||||
def url_check(url):
|
||||
try:
|
||||
result = urlparse(url)
|
||||
if all([result.scheme, result.netloc]):
|
||||
return True
|
||||
else:
|
||||
return False
|
||||
except ValueError:
|
||||
return False
|
||||
|
||||
if not url_check(self.single_dataset__about):
|
||||
raise ConfigurationError(
|
||||
"Must provide an absolute URL for --about. (Example format: http://example.com)"
|
||||
)
|
||||
|
||||
def handle_adaptor(self):
|
||||
self.validate_correct_type_of_configuration_attribute("adaptor__anndata_adaptor__backed", bool)
|
||||
|
||||
def handle_limits(self):
|
||||
self.validate_correct_type_of_configuration_attribute("limits__diffexp_cellcount_max", (type(None), int))
|
||||
self.validate_correct_type_of_configuration_attribute("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
|
||||
Reference in New Issue
Block a user