mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-20 03:18:12 +08:00
8a733270d7
* Fix for favicon with --dataroot * fix static assets in hosted cxg The web proxy at aws eb was not finding the static assets. The solution here is very simple: just copy the directory containing the static assets to the top level of the artifact.zip. This is not really the ideal solution. According to the AWS docs you can make a mapping to the correct location in an an ebextentions config file. I tried this and many combinations but was not able to get this to work following that pattern. Since we control the construction of the zip file, the solution here isn't bad, but it could probably be made better.
226 lines
7.7 KiB
Python
226 lines
7.7 KiB
Python
import os
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import datetime
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from flask import Flask, redirect, current_app, make_response, render_template
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from flask import Blueprint, request, send_from_directory
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from flask_caching import Cache
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from flask_compress import Compress
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from flask_cors import CORS
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from flask_restful import Api, Resource
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from http import HTTPStatus
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import server.common.rest as common_rest
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from server.common.errors import DatasetAccessError
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from server.common.utils import path_join, Float32JSONEncoder
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from server.common.data_locator import DataLocator
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from server.data_common.matrix_loader import MatrixDataLoader, MatrixDataType
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from functools import wraps
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webbp = Blueprint("webapp", "server.common.web", template_folder="templates")
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@webbp.route("/")
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def dataset_index(dataset=None):
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config = current_app.app_config
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if dataset is None:
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if config.datapath:
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location = config.datapath
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else:
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return dataroot_index()
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else:
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location = path_join(config.dataroot, dataset)
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scripts = config.scripts
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try:
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cache_manager = current_app.matrix_data_cache_manager
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with cache_manager.data_adaptor(location, config) as data_adaptor:
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dataset_title = config.get_title(data_adaptor)
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return render_template("index.html", datasetTitle=dataset_title, SCRIPTS=scripts)
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except DatasetAccessError as e:
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return make_response(f"Invalid dataset {dataset}: {str(e)}", HTTPStatus.BAD_REQUEST)
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@webbp.route("/favicon.png")
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def favicon():
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return send_from_directory(os.path.join(webbp.root_path, "static/img/"), "favicon.png")
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def get_data_adaptor(dataset=None):
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config = current_app.app_config
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if dataset is None:
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datapath = config.datapath
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else:
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datapath = path_join(config.dataroot, dataset)
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# path_join returns a normalized path. Therefore it is
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# sufficient to check that the datapath starts with the
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# dataroot to determine that the datapath is under the dataroot.
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if not datapath.startswith(config.dataroot):
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raise DatasetAccessError("Invalid dataset {dataset}")
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if datapath is None:
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return make_response("Dataset must be supplied", HTTPStatus.BAD_REQUEST)
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cache_manager = current_app.matrix_data_cache_manager
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return cache_manager.data_adaptor(datapath, config)
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def rest_get_data_adaptor(func):
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@wraps(func)
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def wrapped_function(self, dataset=None):
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try:
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with get_data_adaptor(dataset) as data_adaptor:
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return func(self, data_adaptor)
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except DatasetAccessError as e:
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return make_response(f"Invalid dataset {dataset}: {str(e)}", HTTPStatus.BAD_REQUEST)
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return wrapped_function
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def static_redirect(dataset, therest):
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""" redirect all static requests to the standard location """
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return redirect(f"/static/{therest}", code=301)
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def dataroot_index():
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# FIXME with a splash screen that includes a listing of all the datasets.
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# or perhaps a login screen if this is a hosted environment,
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# or have a configuration option to redirect to a user specified page.
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# the following is just for demo purposes...
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data = '<!doctype html><html lang="en">'
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data += '<head><title>Hosted Cellxgene</title></head>'
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data += '<body><H1>Welcome to cellxgene</H1>'
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try:
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config = current_app.app_config
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locator = DataLocator(config.dataroot)
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datasets = []
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for fname in locator.ls():
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location = path_join(config.dataroot, fname)
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matrix_data_loader = MatrixDataLoader(location)
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if matrix_data_loader.etype != MatrixDataType.UNKNOWN:
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datasets.append(fname)
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data += '<br/>Select one of these datasets...<br/>'
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data += '<ul>'
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datasets.sort()
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for dataset in datasets:
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data += f'<li><a href={dataset}>{dataset}</a></li>'
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data += '</ul>'
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except Exception as e:
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data += f'<br/>Unable to locate datasets from {config.dataroot}: {str(e)}'
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data += '</body></html>'
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return make_response(data)
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class SchemaAPI(Resource):
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@rest_get_data_adaptor
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def get(self, data_adaptor):
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return common_rest.schema_get(data_adaptor, current_app.annotations)
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class ConfigAPI(Resource):
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@rest_get_data_adaptor
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def get(self, data_adaptor):
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return common_rest.config_get(current_app.app_config, data_adaptor, current_app.annotations)
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class AnnotationsObsAPI(Resource):
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@rest_get_data_adaptor
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def get(self, data_adaptor):
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return common_rest.annotations_obs_get(request, data_adaptor, current_app.annotations)
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@rest_get_data_adaptor
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def put(self, data_adaptor):
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return common_rest.annotations_obs_put(request, data_adaptor, current_app.annotations)
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class AnnotationsVarAPI(Resource):
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@rest_get_data_adaptor
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def get(self, data_adaptor):
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return common_rest.annotations_var_get(request, data_adaptor, current_app.annotations)
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class DataVarAPI(Resource):
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@rest_get_data_adaptor
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def put(self, data_adaptor):
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return common_rest.data_var_put(request, data_adaptor)
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class DiffExpObsAPI(Resource):
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@rest_get_data_adaptor
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def post(self, data_adaptor):
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return common_rest.diffexp_obs_post(request, data_adaptor)
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class LayoutObsAPI(Resource):
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@rest_get_data_adaptor
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def get(self, data_adaptor):
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return common_rest.layout_obs_get(request, data_adaptor)
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@rest_get_data_adaptor
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def put(self, data_adaptor):
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return common_rest.layout_obs_put(request, data_adaptor)
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def get_api_resources(bp_api):
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api = Api(bp_api)
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# Initialization routes
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api.add_resource(SchemaAPI, "/schema")
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api.add_resource(ConfigAPI, "/config")
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# Data routes
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api.add_resource(AnnotationsObsAPI, "/annotations/obs")
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api.add_resource(AnnotationsVarAPI, "/annotations/var")
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api.add_resource(DataVarAPI, "/data/var")
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# Computation routes
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api.add_resource(DiffExpObsAPI, "/diffexp/obs")
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api.add_resource(LayoutObsAPI, "/layout/obs")
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return api
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class Server:
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def __init__(self, matrix_data_cache_manager, annotations, app_config):
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self.app = Flask(__name__, static_folder="../common/web/static")
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self.app.json_encoder = Float32JSONEncoder
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self.cache = Cache(config={"CACHE_TYPE": "simple", "CACHE_DEFAULT_TIMEOUT": 860_000})
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self.cache.init_app(self.app)
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Compress(self.app)
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CORS(self.app, supports_credentials=True)
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# enable session data
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self.app.permanent_session_lifetime = datetime.timedelta(days=50 * 365)
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# Config
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SECRET_KEY = os.environ.get("CXG_SECRET_KEY", default="SparkleAndShine")
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self.app.config.update(SECRET_KEY=SECRET_KEY)
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self.app.register_blueprint(webbp)
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api_version = "/api/v0.2"
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if app_config.datapath:
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bp_api = Blueprint("api", __name__, url_prefix=api_version)
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resources = get_api_resources(bp_api)
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self.app.register_blueprint(resources.blueprint)
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else:
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# NOTE: These routes only allow the dataset to be in the directory
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# of the dataroot, and not a subdirectory. We may want to change
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# the route format at some point
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bp_api = Blueprint("api_dataset", __name__, url_prefix="/<dataset>" + api_version)
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resources = get_api_resources(bp_api)
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self.app.register_blueprint(resources.blueprint)
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self.app.add_url_rule("/<dataset>/", "dataset_index", dataset_index)
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self.app.add_url_rule("/<dataset>/static/<path:therest>", "static_redirect", static_redirect)
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self.app.matrix_data_cache_manager = matrix_data_cache_manager
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self.app.annotations = annotations
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self.app.app_config = app_config
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