mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-21 17:48:13 +08:00
Marcus Kinsella
fb61bd6e9c
This splits the backend into two parts: the local backend for desktop cellxgene and the AWS backend for hosted cellxgene. The local backend is in local_server while the hosted remains in server. The general idea is to copy everything from server to local_server, pull unneeded stuff out of local_server, and keep server as-is for this PR. Not touching server means all the infra and deployment code will continue working just as it did before so we can make those changes incrementally.
121 lines
4.5 KiB
Python
121 lines
4.5 KiB
Python
from local_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_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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