mirror of
https://github.com/chanzuckerberg/cellxgene.git
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f69d141336
This will give us the ability to specify different config options for different dataroots. the key of the dataroot dictionary is no longer the same as the dataroot_url. Previously key==dataroot_url, and now those are separated. Added an "is_multi_dataset" function to simplify logic where it branched on single vs multi. Simplified the rest.py interface by no longer passing in the user annotations object, since that can be retrieved from the dataset.
138 lines
4.4 KiB
Python
138 lines
4.4 KiB
Python
import random
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import shutil
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import string
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import tempfile
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import requests
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import time
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import os
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from subprocess import Popen
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from os import path, popen
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from contextlib import contextmanager
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import pandas as pd
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from server.common.annotations import AnnotationsLocalFile
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from server.common.data_locator import DataLocator
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from server.common.app_config import AppConfig, DEFAULT_SERVER_PORT
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from server.common.utils import find_available_port
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from server.data_common.fbs.matrix import encode_matrix_fbs
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from server.data_common.matrix_loader import MatrixDataLoader, MatrixDataType
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PROJECT_ROOT = popen("git rev-parse --show-toplevel").read().strip()
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def data_with_tmp_annotations(ext: MatrixDataType, annotations_fixture=False):
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tmp_dir = tempfile.mkdtemp()
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annotations_file = path.join(tmp_dir, "test_annotations.csv")
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if annotations_fixture:
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shutil.copyfile(f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k-annotations.csv", annotations_file)
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fname = {
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MatrixDataType.H5AD: f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad",
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MatrixDataType.CXG: "test/test_datasets/pbmc3k.cxg",
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}[ext]
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data_locator = DataLocator(fname)
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config = AppConfig()
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config.update_server_config(
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single_dataset__obs_names=None, single_dataset__var_names=None, single_dataset__datapath=data_locator.path
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)
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config.update_default_dataset_config(
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embeddings__names=["umap"], presentation__max_categories=100, diffexp__lfc_cutoff=0.01,
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)
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config.complete_config()
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data = MatrixDataLoader(data_locator.abspath()).open(config)
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annotations = AnnotationsLocalFile(None, annotations_file)
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return data, tmp_dir, annotations
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def make_fbs(data):
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df = pd.DataFrame(data)
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return encode_matrix_fbs(matrix=df, row_idx=None, col_idx=df.columns)
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def skip_if(condition, reason: str):
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def decorator(f):
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def wraps(self, *args, **kwargs):
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if condition(self):
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self.skipTest(reason)
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else:
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f(self, *args, **kwargs)
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return wraps
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return decorator
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def app_config(data_locator, backed=False, extra_server_config={}, extra_dataset_config={}):
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config = AppConfig()
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config.update_server_config(
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single_dataset__obs_names=None,
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single_dataset__var_names=None,
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adaptor__anndata_adaptor__backed=backed,
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single_dataset__datapath=data_locator,
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limits__diffexp_cellcount_max=None,
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limits__column_request_max=None,
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)
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config.update_default_dataset_config(
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embeddings__names=["umap", "tsne", "pca"], presentation__max_categories=100, diffexp__lfc_cutoff=0.01
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)
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config.update_server_config(**extra_server_config)
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config.update_default_dataset_config(**extra_dataset_config)
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config.complete_config()
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return config
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def random_string(n):
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return "".join(random.choice(string.ascii_letters) for _ in range(n))
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@contextmanager
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def test_server(command_line_args=[], app_config=None):
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"""A context to run the cellxgene server.
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Command line arguments can be passed in, as well as an app_config.
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This function is meant to be used like this, for example:
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with test_server(...) as server:
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r = requests.get(f"{server}/...")
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// check r
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where the server can be accessed within the context, and is terminated when
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the context is exited.
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The port is automatically set using find_available_port.
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The verbose flag is automatically set to True.
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If an app_config is provided, then this function writes a temporary
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yaml config file, which this server will read and parse.
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"""
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port = DEFAULT_SERVER_PORT
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port = find_available_port("localhost", port)
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command = ["cellxgene", "--no-upgrade-check", "launch", "--verbose", "--port=%d" % port] + command_line_args
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tempdir = None
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if app_config:
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tempdir = tempfile.TemporaryDirectory()
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config_file = os.path.join(tempdir.name, "config.yaml")
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app_config.write_config(config_file)
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command.extend(["-c", config_file])
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server = f"http://localhost:{port}"
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ps = Popen(command)
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for _ in range(10):
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try:
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requests.get(f"{server}/health")
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break
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except requests.exceptions.ConnectionError:
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time.sleep(1)
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if tempdir:
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tempdir.cleanup()
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try:
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yield server
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finally:
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try:
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ps.terminate()
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except ProcessLookupError:
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pass
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