mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-22 05:58:12 +08:00
Bruce Martin
0667ad0274
* remove experimental reembedding support * lint * lint * add prepare requirements to requirements-dev * oops, revert accidental deletion of import * more test modifications * remove obsolete unit tests
120 lines
4.5 KiB
Python
120 lines
4.5 KiB
Python
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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"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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"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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