mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-03 07:38:12 +08:00
Introduce a config file to cellxgene (#1264)
* Introduce a config file to cellxgene The config file format is in yaml. The default config is located in server/common/default_config.py. A user may create a yaml file that contains a subset of these fields. It can be used during cellxgene launch, or for hosted cellxgene. The code has also been refactored. Much of the logic to check arguments has moved from launch to app config. It is now possible to set the tiledb context parameters using the config file. Other feature will soon be handled in a similar way.
This commit is contained in:
bmccandless
+338
-63
@@ -1,6 +1,25 @@
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# -*- coding: utf-8 -*-
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from server import __version__ as cellxgene_version
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from flatten_dict import flatten
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from os import mkdir, environ
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from os.path import splitext, basename, isdir
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import sys
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from urllib.parse import urlparse
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import yaml
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from server.common.default_config import get_default_config
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from server.common.errors import ConfigurationError, DatasetAccessError, OntologyLoadFailure
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from server.data_common.matrix_loader import MatrixDataLoader, MatrixDataCacheManager, MatrixDataType
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from server.common.utils import find_available_port, is_port_available
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import warnings
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from server.common.annotations import AnnotationsLocalFile
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from server.common.utils import custom_format_warning
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DEFAULT_SERVER_PORT = int(environ.get("CXG_SERVER_PORT", "5005"))
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# anything bigger than this will generate a special message
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BIG_FILE_SIZE_THRESHOLD = 100 * 2 ** 20 # 100MB
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class AppFeature(object):
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@@ -19,78 +38,334 @@ class AppFeature(object):
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class AppConfig(object):
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def __init__(self, **kw):
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super().__init__()
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def __init__(self):
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# app inputs
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self.datapath = None
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self.dataroot = None
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self.title = ""
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self.about = None
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self.scripts = []
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self.layout = []
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self.max_category_items = 100
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self.diffexp_lfc_cutoff = 0.01
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self.disable_diffexp = False
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self.enable_reembedding = False
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self.anndata_backed = False
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self.default_config = get_default_config()
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# The index page when in multi-dataset mode:
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# False or None: this returns a 404 code
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# True: loads a test index page, which links to the datasets that are available in the dataroot
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# string/URL: redirect to this URL: flask.redirect(config.multi_dataset_index)
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self.multi_dataset_index = False
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dc = self.default_config
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try:
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self.server__verbose = dc["server"]["verbose"]
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self.server__debug = dc["server"]["debug"]
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self.server__host = dc["server"]["host"]
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self.server__port = dc["server"]["port"]
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self.server__scripts = dc["server"]["scripts"]
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self.server__open_browser = dc["server"]["open_browser"]
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self.multi_dataset__dataroot = dc["multi_dataset"]["dataroot"]
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self.multi_dataset__index = dc["multi_dataset"]["index"]
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self.multi_dataset__allowed_matrix_types = dc["multi_dataset"]["allowed_matrix_types"]
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self.single_dataset__datapath = dc["single_dataset"]["datapath"]
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self.single_dataset__obs_names = dc["single_dataset"]["obs_names"]
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self.single_dataset__var_names = dc["single_dataset"]["var_names"]
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self.single_dataset__about = dc["single_dataset"]["about"]
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self.single_dataset__title = dc["single_dataset"]["title"]
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self.user_annotations__enable = dc["user_annotations"]["enable"]
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self.user_annotations__type = dc["user_annotations"]["type"]
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self.user_annotations__local_file_csv__directory = dc["user_annotations"]["local_file_csv"]["directory"]
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self.user_annotations__local_file_csv__file = dc["user_annotations"]["local_file_csv"]["file"]
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self.user_annotations__ontology__enable = dc["user_annotations"]["ontology"]["enable"]
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self.user_annotations__ontology__obo_location = dc["user_annotations"]["ontology"]["obo_location"]
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self.presentation__max_categories = dc["presentation"]["max_categories"]
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self.embeddings__names = dc["embeddings"]["names"]
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self.embeddings__enable_reembedding = dc["embeddings"]["enable_reembedding"]
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self.diffexp__enable = dc["diffexp"]["enable"]
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self.diffexp__lfc_cutoff = dc["diffexp"]["lfc_cutoff"]
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self.adaptor__cxg_adaptor__tiledb_ctx = dc["adaptor"]["cxg_adaptor"]["tiledb_ctx"]
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self.adaptor__anndata_adaptor__backed = dc["adaptor"]["anndata_adaptor"]["backed"]
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except KeyError as e:
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raise ConfigurationError(f"Unexpected config: {str(e)}")
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# A list of allowed matrix types. If an empty list, then all matrix types are allowed
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self.multi_dataset_allowed_matrix_type = []
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# The annotation object is created during complete_config and stored here.
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self.user_annotations = None
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# TODO these options may not apply to all datasets in the multi dataset.
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# may need to invent a way to associate these config parameters with
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# specific datasets.
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self.obs_names = None
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self.var_names = None
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# Set to true when config_completed is called
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self.is_completed = False
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# parameters
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self.diffexp_may_be_slow = False
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def update_from_config_file(self, config_file):
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with open(config_file) as fyaml:
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config = yaml.load(fyaml, Loader=yaml.FullLoader)
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inputs = [
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"datapath",
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"dataroot",
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"title",
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"about",
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"scripts",
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"layout",
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"max_category_items",
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"diffexp_lfc_cutoff",
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"obs_names",
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"var_names",
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"anndata_backed",
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"disable_diffexp",
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"enable_reembedding",
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"multi_dataset_index",
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"multi_dataset_allowed_matrix_type",
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]
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# special case for tiledb_ctx whose value is a dict, and cannot
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# be handled by the flattening below
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if config.get("adaptor", {}).get("cxg_adaptor", {}).get("tiledb_ctx"):
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value = config["adaptor"]["cxg_adaptor"]["tiledb_ctx"]
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self.adaptor__cxg_adaptor__tiledb_ctx = value
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del config["adaptor"]["cxg_adaptor"]["tiledb_ctx"]
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self.update(inputs, kw)
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flat_config = flatten(config)
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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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if not hasattr(self, attr):
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raise ConfigurationError(f"Unknown key from config file: {key}")
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try:
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setattr(self, attr, value)
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except KeyError:
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raise ConfigurationError(f"Unable to set config attribute: {key}")
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def update(self, inputs, kw):
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for k, v in kw.items():
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if k in inputs:
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setattr(self, k, v)
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else:
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raise RuntimeError(f"unknown config parameter {k}.")
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self.is_completed = False
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def update(self, **kw):
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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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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.is_completed = False
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def complete_config(self, matrix_data_cache_manager=None, 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 matrix_data_cache_manager is None:
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matrix_data_cache_manager = MatrixDataCacheManager()
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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(matrix_cache=matrix_data_cache_manager, messagefn=messagefn)
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self.handle_server(context)
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self.handle_single_dataset(context)
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self.handle_multi_dataset(context)
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self.handle_user_annotations(context)
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self.handle_embeddings(context)
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self.handle_diffexp(context)
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self.handle_adaptor(context)
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self.is_completed = True
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def __check_attr(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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def handle_server(self, context):
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self.__check_attr("server__verbose", bool)
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self.__check_attr("server__debug", bool)
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self.__check_attr("server__host", str)
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self.__check_attr("server__port", (type(None), int))
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self.__check_attr("server__scripts", (list, tuple))
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self.__check_attr("server__open_browser", bool)
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if self.server__port:
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if self.server__debug:
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raise ConfigurationError(
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"'port' and 'debug' may not be used together (try 'verbose' for error logging)."
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)
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if not is_port_available(self.server__host, self.server__port):
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raise ConfigurationError(
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f"The port selected {self.server__port} is in use, please configure an open port."
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)
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else:
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self.server__port = find_available_port(self.server__host, DEFAULT_SERVER_PORT)
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if self.server__debug:
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context["messagefn"]("in debug mode, setting verbose=True and open_browser=False")
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self.server__verbose = True
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self.server__open_browser = False
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else:
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warnings.formatwarning = custom_format_warning
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if not self.server__verbose:
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sys.tracebacklimit = 0
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def handle_presentation(self, context):
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self.__check_attr("presentation__max_categories", int)
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def handle_single_dataset(self, context):
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self.__check_attr("single_dataset__datapath", (str, type(None)))
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self.__check_attr("single_dataset__title", (str, type(None)))
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self.__check_attr("single_dataset__about", (str, type(None)))
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self.__check_attr("single_dataset__obs_names", (str, type(None)))
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self.__check_attr("single_dataset__var_names", (str, type(None)))
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if self.single_dataset__datapath is None:
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if self.multi_dataset__dataroot is None:
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# TODO: change the error message once dataroot is fully supported
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raise ConfigurationError("missing datapath")
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return
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else:
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if self.multi_dataset__dataroot is not None:
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raise ConfigurationError("must supply only one of datapath or dataroot")
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# preload this data set
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matrix_data_loader = MatrixDataLoader(self.single_dataset__datapath)
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try:
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matrix_data_loader.pre_load_validation()
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except DatasetAccessError as e:
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raise ConfigurationError(str(e))
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file_size = matrix_data_loader.file_size()
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file_basename = basename(self.single_dataset__datapath)
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if file_size > BIG_FILE_SIZE_THRESHOLD:
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context["messagefn"](f"Loading data from {file_basename}, this may take a while...")
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else:
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context["messagefn"](f"Loading data from {file_basename}.")
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if self.single_dataset__about:
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def url_check(url):
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try:
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result = urlparse(url)
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if all([result.scheme, result.netloc]):
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return True
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else:
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return False
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except ValueError:
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return False
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if not url_check(self.single_dataset__about):
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raise ConfigurationError(
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"Must provide an absolute URL for --about. (Example format: http://example.com)"
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)
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def handle_multi_dataset(self, context):
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self.__check_attr("multi_dataset__dataroot", (type(None), str))
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self.__check_attr("multi_dataset__index", (type(None), bool, str))
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self.__check_attr("multi_dataset__allowed_matrix_types", (list))
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if self.multi_dataset__dataroot is None:
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return
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# error checking
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for mtype in self.multi_dataset__allowed_matrix_types:
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try:
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MatrixDataType(mtype)
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except ValueError:
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raise ConfigurationError(f'Invalid matrix type in "allowed_matrix_types": {mtype}')
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def handle_user_annotations(self, context):
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self.__check_attr("user_annotations__enable", bool)
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self.__check_attr("user_annotations__type", str)
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self.__check_attr("user_annotations__local_file_csv__directory", (type(None), str))
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self.__check_attr("user_annotations__local_file_csv__file", (type(None), str))
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self.__check_attr("user_annotations__ontology__enable", bool)
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self.__check_attr("user_annotations__ontology__obo_location", (type(None), str))
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if self.user_annotations__enable:
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# TODO, replace this with a factory pattern once we have more than one way
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# to do annotations. currently only local_file_csv
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if self.user_annotations__type != "local_file_csv":
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raise ConfigurationError('The only annotation type support is "local_file_csv"')
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dirname = self.user_annotations__local_file_csv__directory
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filename = self.user_annotations__local_file_csv__file
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if filename is not None and dirname is not None:
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raise ConfigurationError("'annotations-file' and 'annotations-dir' may not be used together.")
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if filename is not None:
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lf_name, lf_ext = splitext(filename)
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if lf_ext and lf_ext != ".csv":
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raise ConfigurationError(f"annotation file type must be .csv: {filename}")
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if dirname is not None and not isdir(dirname):
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try:
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mkdir(dirname)
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except OSError:
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raise ConfigurationError("Unable to create directory specified by --annotations-dir")
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self.user_annotations = AnnotationsLocalFile(dirname, filename)
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# if the user has specified a fixed label file, go ahead and validate it
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# so that we can remove errors early in the process.
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if self.single_dataset__datapath and self.user_annotations__local_file_csv__file:
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with context["matrix_cache"].data_adaptor(self.single_dataset__datapath, self) as data_adaptor:
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data_adaptor.check_new_labels(self.user_annotations.read_labels(data_adaptor))
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if self.user_annotations__ontology__enable or self.user_annotations__ontology__obo_location:
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try:
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self.user_annotations.load_ontology(self.user_annotations__ontology__obo_location)
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except OntologyLoadFailure as e:
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raise ConfigurationError("Unable to load ontology terms\n" + str(e))
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else:
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if self.user_annotations__type == "local_file_csv":
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dirname = self.user_annotations__local_file_csv__directory
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filename = self.user_annotations__local_file_csv__file
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if filename is not None:
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context["messsagefn"]("Warning: --annotations-file ignored as annotations are disabled.")
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if dirname is not None:
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context["messagefn"]("Warning: --annotations-dir ignored as annotations are disabled.")
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if self.user_annotations__ontology__enable:
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context["messagefn"](
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"Warning: --experimental-annotations-ontology" " ignored as annotations are disabled."
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)
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if self.user_annotations__ontology__obo_location is not None:
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context["messagefn"](
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"Warning: --experimental-annotations-ontology-obo" " ignored as annotations are disabled."
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)
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def handle_embeddings(self, context):
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self.__check_attr("embeddings__names", (list, tuple))
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self.__check_attr("embeddings__enable_reembedding", bool)
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if self.single_dataset__datapath:
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if self.embeddings__enable_reembedding:
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matrix_data_loader = MatrixDataLoader(self.single_dataset__datapath)
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if matrix_data_loader.matrix_data_type() != MatrixDataType.H5AD:
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raise ConfigurationError("'enable-reembedding is only supported with H5AD files.")
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if self.adaptor__anndata_adaptor__backed:
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raise ConfigurationError("enable-reembedding is not supported when run in --backed mode.")
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def handle_diffexp(self, context):
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self.__check_attr("diffexp__enable", bool)
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self.__check_attr("diffexp__lfc_cutoff", float)
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if self.single_dataset__datapath:
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with context["matrix_cache"].data_adaptor(self.single_dataset__datapath, self) as data_adaptor:
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if self.diffexp__enable and data_adaptor.parameters.get("diffexp_may_be_slow", False):
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context["messagefn"](
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f"CAUTION: due to the size of your dataset, "
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f"running differential expression may take longer or fail."
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)
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def handle_adaptor(self, context):
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# cxg
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self.__check_attr("adaptor__cxg_adaptor__tiledb_ctx", dict)
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from server.data_cxg.cxg_adaptor import CxgAdaptor
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CxgAdaptor.set_tiledb_context(self.adaptor__cxg_adaptor__tiledb_ctx)
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# anndata
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self.__check_attr("adaptor__anndata_adaptor__backed", bool)
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def get_title(self, data_adaptor):
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return self.title if self.title else data_adaptor.get_title()
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return self.single_dataset__title if self.single_dataset__title else data_adaptor.get_title()
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def get_about(self, data_adaptor):
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return self.about if self.about else data_adaptor.get_about()
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return self.single_dataset__about if self.single_dataset__about else data_adaptor.get_about()
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def get_config(self, data_adaptor, annotation=None):
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def get_client_config(self, data_adaptor, annotation=None):
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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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# 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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if not self.is_completed:
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raise ConfigurationError("The configuration has not been completed")
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# features
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features = [f.todict() for f in data_adaptor.get_features(annotation)]
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|
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@@ -110,14 +385,14 @@ class AppConfig(object):
|
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|
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# parameters
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parameters = {
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"layout": self.layout,
|
||||
"max-category-items": self.max_category_items,
|
||||
"obs_names": self.obs_names,
|
||||
"var_names": self.var_names,
|
||||
"diffexp_lfc_cutoff": self.diffexp_lfc_cutoff,
|
||||
"backed": self.anndata_backed,
|
||||
"disable-diffexp": self.disable_diffexp,
|
||||
"enable-reembedding": self.enable_reembedding,
|
||||
"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,
|
||||
|
||||
@@ -0,0 +1,67 @@
|
||||
import yaml
|
||||
|
||||
default_config = """
|
||||
# cellxgene configuration
|
||||
|
||||
server:
|
||||
verbose: false
|
||||
debug: false
|
||||
host: "127.0.0.1"
|
||||
port : null
|
||||
scripts : []
|
||||
open_browser: false
|
||||
|
||||
presentation:
|
||||
max_categories: 1000
|
||||
|
||||
multi_dataset:
|
||||
dataroot: null
|
||||
|
||||
# The index page when in multi-dataset mode:
|
||||
# false or null: this returns a 404 code
|
||||
# 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
|
||||
|
||||
# A list of allowed matrix types. If an empty list, then all matrix types are allowed
|
||||
allowed_matrix_types: []
|
||||
|
||||
single_dataset:
|
||||
datapath: null
|
||||
obs_names: null
|
||||
var_names: null
|
||||
about: null
|
||||
title: null
|
||||
|
||||
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
|
||||
|
||||
adaptor:
|
||||
cxg_adaptor:
|
||||
tiledb_ctx:
|
||||
sm.tile_cache_size: 8589934592
|
||||
sm.num_reader_threads: 32
|
||||
vfs.s3.region: us-east-1
|
||||
|
||||
anndata_adaptor:
|
||||
backed: false
|
||||
"""
|
||||
|
||||
|
||||
def get_default_config():
|
||||
return yaml.load(default_config, Loader=yaml.Loader)
|
||||
@@ -60,3 +60,11 @@ class OntologyLoadFailure(Exception):
|
||||
"""
|
||||
|
||||
pass
|
||||
|
||||
|
||||
class ConfigurationError(Exception):
|
||||
"""
|
||||
Raised when checking configuration errors
|
||||
"""
|
||||
|
||||
pass
|
||||
|
||||
@@ -33,7 +33,7 @@ def schema_get(data_adaptor, annotations):
|
||||
|
||||
|
||||
def config_get(app_config, data_adaptor, annotations):
|
||||
config = app_config.get_config(data_adaptor, annotations)
|
||||
config = app_config.get_client_config(data_adaptor, annotations)
|
||||
return make_response(jsonify(config), HTTPStatus.OK)
|
||||
|
||||
|
||||
@@ -131,7 +131,7 @@ def data_var_put(request, data_adaptor):
|
||||
|
||||
|
||||
def diffexp_obs_post(request, data_adaptor):
|
||||
if data_adaptor.config.disable_diffexp:
|
||||
if not data_adaptor.config.diffexp__enable:
|
||||
return make_response(f"diffexp not supported.", HTTPStatus.BAD_REQUEST)
|
||||
|
||||
args = request.get_json()
|
||||
@@ -198,7 +198,7 @@ def layout_obs_put(request, data_adaptor):
|
||||
preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
|
||||
if preferred_mimetype != "application/octet-stream":
|
||||
return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
|
||||
if not data_adaptor.config.enable_reembedding:
|
||||
if not data_adaptor.config.embedding__enable_reembedding:
|
||||
return make_response(f"Computed embedding not supported.", HTTPStatus.BAD_REQUEST)
|
||||
|
||||
args = request.get_json()
|
||||
|
||||
Reference in New Issue
Block a user