from server import display_version as cellxgene_display_version def get_client_config(app_config, data_adaptor): """ Return the configuration as required by the /config REST route """ server_config = app_config.server_config dataset_config = data_adaptor.dataset_config annotation = dataset_config.user_annotations # FIXME The current set of config is not consistently presented: # we have camalCase, hyphen-text, and underscore_text # make sure the configuration has been checked. app_config.check_config() # display_names title = app_config.get_title(data_adaptor) about = app_config.get_about(data_adaptor) display_names = dict(engine=data_adaptor.get_name(), dataset=title) # library_versions library_versions = {} library_versions.update(data_adaptor.get_library_versions()) library_versions["cellxgene"] = cellxgene_display_version # links links = {"about-dataset": about} # parameters parameters = { "layout": dataset_config.embeddings__names, "max-category-items": dataset_config.presentation__max_categories, "obs_names": server_config.single_dataset__obs_names, "var_names": server_config.single_dataset__var_names, "diffexp_lfc_cutoff": dataset_config.diffexp__lfc_cutoff, "backed": server_config.adaptor__anndata_adaptor__backed, "disable-diffexp": not dataset_config.diffexp__enable, "annotations": False, "annotations_file": None, "annotations_dir": None, "annotations_genesets": True, # feature flag "annotations_genesets_readonly": dataset_config.user_annotations__gene_sets__readonly, "annotations_genesets_summary_methods": ["mean"], "custom_colors": dataset_config.presentation__custom_colors, "diffexp-may-be-slow": False, } # corpora dataset_props # TODO/Note: putting info from the dataset into the /config is not ideal. # However, it is definitely not part of /schema, and we do not have a top-level # route for data properties. Consider creating one at some point. corpora_props = data_adaptor.get_corpora_props() if corpora_props and "default_embedding" in corpora_props: default_embedding = corpora_props["default_embedding"] if isinstance(default_embedding, str) and default_embedding.startswith("X_"): default_embedding = default_embedding[2:] # drop X_ prefix if default_embedding in data_adaptor.get_embedding_names(): parameters["default_embedding"] = default_embedding data_adaptor.update_parameters(parameters) if annotation: annotation.update_parameters(parameters, data_adaptor) # gather it all together client_config = {} config = client_config["config"] = {} config["displayNames"] = display_names config["library_versions"] = library_versions config["links"] = links config["parameters"] = parameters config["corpora_props"] = corpora_props config["limits"] = { "column_request_max": server_config.limits__column_request_max, "diffexp_cellcount_max": server_config.limits__diffexp_cellcount_max, } return client_config