mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-27 03:58:11 +08:00
server refactor (#1140)
This PR contains a refactoring to make adding new features easier. The new features include supporting the tiledb format, and the multi dataset application. The refactoring includes Simplifying the directory structure and files. a class structure to handle annotations (currently one type: AnnotationsLocalFile). a class to handle application configuration a class structure to handle matrix data (currently AnndataAdaptor and CxgAdaptor). CxgAdaptor uses tiledb. Algorithms that were previously dependent on the scanpy anndata object are now generalized to work with an abstract interface. The multi dataset option is not fully supported yet, and so the option to use it is hidden. Use "cli launch --dataroot ..." To access this feature. All combinations of app single dataset/ app multi dataset and AnndataAdaptor/CxgAdaptor work with all the features, such as annotations, ontologies, diffexp.
This commit is contained in:
bmccandless
+274
-245
@@ -10,67 +10,20 @@ from urllib.parse import urlparse
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import click
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from server.app.app import Server
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from server.app.util.errors import ScanpyFileError
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from server.app.util.utils import custom_format_warning
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from server.utils.utils import find_available_port, is_port_available, sort_options
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from server.app.util.data_locator import DataLocator
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from server.app.util.ontology import load_obo, OntologyLoadFailure
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from server.common.utils import custom_format_warning
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from server.common.utils import find_available_port, is_port_available, sort_options
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from server.data_common.matrix_loader import MatrixDataLoader, MatrixDataCacheManager
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from server.common.annotations import AnnotationsLocalFile
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from server.common.app_config import AppConfig
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from server.common.errors import OntologyLoadFailure
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# anything bigger than this will generate a special message
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BIG_FILE_SIZE_THRESHOLD = 100 * 2 ** 20 # 100MB
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DEFAULT_SERVER_PORT = int(environ.get('CXG_SERVER_PORT', '5005'))
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def common_args(func):
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"""
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Decorator to contain CLI args that will be common to both CLI and GUI: title and engine args.
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"""
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@click.option("--title", "-t", metavar="<text>", help="Title to display. If omitted will use file name.")
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@click.option(
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"--about",
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metavar="<URL>",
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help="URL providing more information about the dataset " "(hint: must be a fully specified absolute URL).",
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)
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@click.option(
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"--embedding",
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"-e",
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default=[],
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multiple=True,
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show_default=False,
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metavar="<text>",
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help="Embedding name, eg, 'umap'. Repeat option for multiple embeddings. Defaults to all.",
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)
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@click.option(
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"--obs-names",
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"-obs",
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default=None,
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metavar="<text>",
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help="Name of annotation field to use for observations. If not specified cellxgene will use the the obs index.",
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)
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@click.option(
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"--var-names",
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"-var",
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default=None,
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metavar="<text>",
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help="Name of annotation to use for variables. If not specified cellxgene will use the the var index.",
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)
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@click.option(
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"--max-category-items",
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default=1000,
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metavar="<integer>",
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show_default=True,
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help="Will not display categories with more distinct values than specified.",
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)
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@click.option(
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"--diffexp-lfc-cutoff",
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"-de",
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default=0.01,
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show_default=True,
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metavar="<float>",
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help="Minimum log fold change threshold for differential expression.",
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)
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def annotation_args(func):
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@click.option(
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"--experimental-annotations",
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is_flag=True,
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@@ -101,27 +54,14 @@ def common_args(func):
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is_flag=True,
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default=False,
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show_default=True,
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help="When creating annotations, optionally autocomplete names from ontology terms.",)
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help="When creating annotations, optionally autocomplete names from ontology terms."
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)
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@click.option(
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"--experimental-annotations-ontology-obo",
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default=None,
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show_default=True,
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metavar="<path or url>",
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help="Location of OBO file defining cell annotatoin autosuggest terms.",)
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@click.option(
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"--backed",
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"-b",
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is_flag=True,
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default=False,
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show_default=False,
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help="Load data in file-backed mode. This may save memory, but may result in slower overall performance.",
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)
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@click.option(
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"--disable-diffexp",
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is_flag=True,
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default=False,
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show_default=False,
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help="Disable on-demand differential expression.",
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help="Location of OBO file defining cell annotation autosuggest terms."
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)
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@functools.wraps(func)
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def wrapper(*args, **kwargs):
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@@ -130,41 +70,188 @@ def common_args(func):
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return wrapper
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def parse_engine_args(
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embedding,
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obs_names,
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var_names,
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max_category_items,
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diffexp_lfc_cutoff,
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experimental_annotations,
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experimental_annotations_file,
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experimental_annotations_output_dir,
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backed,
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disable_diffexp,
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experimental_annotations_ontology,
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experimental_annotations_ontology_obo
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):
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annotations_file = experimental_annotations_file if experimental_annotations else None
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annotations_output_dir = experimental_annotations_output_dir if experimental_annotations else None
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annotations_cell_ontology_enabled = experimental_annotations and (
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experimental_annotations_ontology or bool(experimental_annotations_ontology_obo)
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def config_args(func):
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@click.option(
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"--max-category-items",
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default=1000,
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metavar="<integer>",
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show_default=True,
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help="Will not display categories with more distinct values than specified.",
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)
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annotations_ontology_obopath = experimental_annotations_ontology_obo if annotations_cell_ontology_enabled else None
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return {
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"layout": embedding,
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"max_category_items": max_category_items,
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"diffexp_lfc_cutoff": diffexp_lfc_cutoff,
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"obs_names": obs_names,
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"var_names": var_names,
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"annotations": experimental_annotations,
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"annotations_file": annotations_file,
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"annotations_output_dir": annotations_output_dir,
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"annotations_cell_ontology_enabled": annotations_cell_ontology_enabled,
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"annotations_cell_ontology_obopath": annotations_ontology_obopath,
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"annotations_cell_ontology_terms": None,
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"backed": backed,
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"disable_diffexp": disable_diffexp,
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}
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@click.option(
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"--diffexp-lfc-cutoff",
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"-de",
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default=0.01,
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show_default=True,
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metavar="<float>",
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help="Minimum log fold change threshold for differential expression.",
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)
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@click.option(
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"--disable-diffexp",
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is_flag=True,
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default=False,
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show_default=False,
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help="Disable on-demand differential expression.",
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)
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@click.option(
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"--embedding",
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"-e",
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default=[],
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multiple=True,
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show_default=False,
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metavar="<text>",
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help="Embedding name, eg, 'umap'. Repeat option for multiple embeddings. Defaults to all.",
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)
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@functools.wraps(func)
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def wrapper(*args, **kwargs):
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return func(*args, **kwargs)
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return wrapper
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def dataset_args(func):
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@click.option(
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"--obs-names",
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"-obs",
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default=None,
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metavar="<text>",
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help="Name of annotation field to use for observations. If not specified cellxgene will use the the obs index.",
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)
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@click.option(
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"--var-names",
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"-var",
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default=None,
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metavar="<text>",
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help="Name of annotation to use for variables. If not specified cellxgene will use the the var index.",
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)
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@click.option(
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"--backed",
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"-b",
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is_flag=True,
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default=False,
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show_default=False,
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help="Load anndata in file-backed mode. "
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"This may save memory, but may result in slower overall performance.",
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)
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@click.option(
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"--title",
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"-t",
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metavar="<text>",
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help="Title to display. If omitted will use file name."
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)
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@click.option(
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"--about",
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metavar="<URL>",
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help="URL providing more information about the dataset " "(hint: must be a fully specified absolute URL).",
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)
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@functools.wraps(func)
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def wrapper(*args, **kwargs):
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return func(*args, **kwargs)
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return wrapper
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def server_args(func):
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@click.option(
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"--debug",
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"-d",
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is_flag=True,
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default=False,
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show_default=True,
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help="Run in debug mode. This is helpful for cellxgene developers, "
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"or when you want more information about an error condition.",
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)
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@click.option(
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"--verbose",
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"-v",
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is_flag=True,
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default=False,
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show_default=True,
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help="Provide verbose output, including warnings and all server requests.",
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)
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@click.option(
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"--port",
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"-p",
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metavar="<port>",
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default=DEFAULT_SERVER_PORT,
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show_default=True,
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help="Port to run server on. If not specified cellxgene will find an available port.",
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)
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@click.option(
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"--host",
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metavar="<IP address>",
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default="127.0.0.1",
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show_default=False,
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help="Host IP address. By default cellxgene will use localhost (e.g. 127.0.0.1).",
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)
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@click.option(
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"--scripts",
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"-s",
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default=[],
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multiple=True,
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metavar="<text>",
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help="Additional script files to include in HTML page. If not specified, "
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"no additional script files will be included.",
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show_default=False,
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)
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@functools.wraps(func)
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def wrapper(*args, **kwargs):
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return func(*args, **kwargs)
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return wrapper
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def launch_args(func):
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@annotation_args
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@config_args
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@dataset_args
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@server_args
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@click.option(
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"--dataroot",
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default=None,
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metavar="<data directory>",
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help="Enable cellxgene to serve multiple files. Supply path (local directory or URL)"
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" to folder containing H5AD and/or CXG datasets.",
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hidden=True) # TODO, unhide when dataroot is supported)
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@click.argument("datapath", required=False, metavar="<path to data file>")
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@click.option(
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"--open",
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"-o",
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"open_browser",
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is_flag=True,
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default=False,
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show_default=True,
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help="Open web browser after launch.",
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)
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@click.help_option("--help", "-h", help="Show this message and exit.")
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@functools.wraps(func)
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def wrapper(*args, **kwargs):
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return func(*args, **kwargs)
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return wrapper
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def handle_scripts(scripts):
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if scripts:
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click.echo(
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r"""
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/ / /\ \ \__ _ _ __ _ __ (_)_ __ __ _
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\ \/ \/ / _` | '__| '_ \| | '_ \ / _` |
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\ /\ / (_| | | | | | | | | | | (_| |
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\/ \/ \__,_|_| |_| |_|_|_| |_|\__, |
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|___/
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The --scripts flag is intended for developers to include google analytics etc. You could be opening yourself to a
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security risk by including the --scripts flag. Make sure you trust the scripts that you are including.
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"""
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)
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scripts_pretty = ", ".join(scripts)
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click.confirm(f"Are you sure you want to inject these scripts: {scripts_pretty}?", abort=True)
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def handle_verbose(verbose):
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if not verbose:
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sys.tracebacklimit = 0
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@sort_options
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@@ -172,62 +259,10 @@ def parse_engine_args(
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short_help="Launch the cellxgene data viewer. " "Run `cellxgene launch --help` for more information.",
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options_metavar="<options>",
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)
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@click.argument("data", nargs=1, metavar="<path to data file>", required=True)
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@click.option(
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"--verbose",
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"-v",
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is_flag=True,
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default=False,
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show_default=True,
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help="Provide verbose output, including warnings and all server requests.",
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)
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@click.option(
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"--debug",
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"-d",
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is_flag=True,
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default=False,
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show_default=True,
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help="Run in debug mode. This is helpful for cellxgene developers, "
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"or when you want more information about an error condition.",
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)
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@click.option(
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"--open",
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"-o",
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"open_browser",
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is_flag=True,
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default=False,
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show_default=True,
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help="Open web browser after launch.",
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)
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@click.option(
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"--port",
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"-p",
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metavar="<port>",
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default=DEFAULT_SERVER_PORT,
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show_default=True,
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help="Port to run server on. If not specified cellxgene will find an available port.",
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)
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@click.option(
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"--host",
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metavar="<IP address>",
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default="127.0.0.1",
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show_default=False,
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help="Host IP address. By default cellxgene will use localhost (e.g. 127.0.0.1).",
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)
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@click.option(
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"--scripts",
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"-s",
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default=[],
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multiple=True,
|
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metavar="<text>",
|
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help="Additional script files to include in HTML page. If not specified, "
|
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"no additional script files will be included.",
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show_default=False,
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)
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@click.help_option("--help", "-h", help="Show this message and exit.")
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@common_args
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@launch_args
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def launch(
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data,
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datapath,
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dataroot,
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verbose,
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debug,
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open_browser,
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@@ -257,47 +292,41 @@ def launch(
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Examples:
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> cellxgene launch example_dataset/pbmc3k.h5ad --title pbmc3k
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> cellxgene launch example-dataset/pbmc3k.h5ad --title pbmc3k
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> cellxgene launch <your data file> --title <your title>
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> cellxgene launch <url>"""
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e_args = parse_engine_args(
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embedding,
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obs_names,
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var_names,
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max_category_items,
|
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diffexp_lfc_cutoff,
|
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experimental_annotations,
|
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experimental_annotations_file,
|
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experimental_annotations_output_dir,
|
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backed,
|
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disable_diffexp,
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experimental_annotations_ontology,
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experimental_annotations_ontology_obo,
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)
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try:
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data_locator = DataLocator(data)
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except RuntimeError as re:
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raise click.ClickException(f"Unable to access data at {data}. {str(re)}")
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# TODO Examples to provide when "--dataroot" is unhidden
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# > cellxgene launch --dataroot example-dataset/
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#
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# > cellxgene launch --dataroot <url>
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# Startup message
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click.echo("[cellxgene] Starting the CLI...")
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# Argument checking
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if data_locator.islocal():
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# if data locator is local, apply file system conventions and other "cheap"
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# validation checks. If a URI, defer until we actually fetch the data and
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# try to read it. Many of these tests don't make sense for URIs (eg, extension-
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# based typing).
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if not data_locator.exists():
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raise click.FileError(data, hint="file does not exist")
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if not data_locator.isfile():
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raise click.FileError(data, hint="data is not a file")
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name, extension = splitext(data)
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if extension != ".h5ad":
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raise click.FileError(basename(data), hint="file type must be .h5ad")
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if datapath is None and dataroot is None:
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# TODO: change the error message once dataroot is fully supported
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raise click.ClickException("Missing argument \"<path to data file>.\"")
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# raise click.ClickException("must supply either <path to data file> or --dataroot")
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||||
if datapath is not None and dataroot is not None:
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||||
raise click.ClickException("must supply only one of <path to data file> or --dataroot")
|
||||
|
||||
if datapath:
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||||
# preload this data set
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||||
matrix_data_loader = MatrixDataLoader(datapath)
|
||||
|
||||
try:
|
||||
matrix_data_loader.pre_load_validation()
|
||||
except RuntimeError as e:
|
||||
raise click.ClickException(str(e))
|
||||
|
||||
file_size = matrix_data_loader.file_size()
|
||||
if file_size > BIG_FILE_SIZE_THRESHOLD:
|
||||
click.echo(f"[cellxgene] Loading data from {basename(datapath)}, this may take a while...")
|
||||
else:
|
||||
click.echo(f"[cellxgene] Loading data from {basename(datapath)}.")
|
||||
|
||||
if debug:
|
||||
verbose = True
|
||||
@@ -305,26 +334,11 @@ def launch(
|
||||
else:
|
||||
warnings.formatwarning = custom_format_warning
|
||||
|
||||
if not verbose:
|
||||
sys.tracebacklimit = 0
|
||||
handle_verbose(verbose)
|
||||
handle_scripts(scripts)
|
||||
|
||||
if scripts:
|
||||
click.echo(
|
||||
r"""
|
||||
/ / /\ \ \__ _ _ __ _ __ (_)_ __ __ _
|
||||
\ \/ \/ / _` | '__| '_ \| | '_ \ / _` |
|
||||
\ /\ / (_| | | | | | | | | | | (_| |
|
||||
\/ \/ \__,_|_| |_| |_|_|_| |_|\__, |
|
||||
|___/
|
||||
The --scripts flag is intended for developers to include google analytics etc. You could be opening yourself to a
|
||||
security risk by including the --scripts flag. Make sure you trust the scripts that you are including.
|
||||
"""
|
||||
)
|
||||
scripts_pretty = ", ".join(scripts)
|
||||
click.confirm(f"Are you sure you want to inject these scripts: {scripts_pretty}?", abort=True)
|
||||
|
||||
if not title:
|
||||
file_parts = splitext(basename(data))
|
||||
if not title and datapath is not None:
|
||||
file_parts = splitext(basename(datapath))
|
||||
title = file_parts[0]
|
||||
|
||||
if port:
|
||||
@@ -365,16 +379,7 @@ def launch(
|
||||
"Unable to create directory specified by " "--experimental-annotations-output-dir"
|
||||
)
|
||||
|
||||
if e_args.get('annotations_cell_ontology_enabled', False):
|
||||
try:
|
||||
e_args['annotations_cell_ontology_terms'] = load_obo(
|
||||
e_args.get('annotations_cell_ontology_obopath', None)
|
||||
)
|
||||
except OntologyLoadFailure as e:
|
||||
raise click.ClickException("Unable to load ontology terms\n" + str(e))
|
||||
|
||||
if about:
|
||||
|
||||
def url_check(url):
|
||||
try:
|
||||
result = urlparse(url)
|
||||
@@ -391,37 +396,61 @@ def launch(
|
||||
# Setup app
|
||||
cellxgene_url = f"http://{host}:{port}"
|
||||
|
||||
# Import Flask app
|
||||
server = Server()
|
||||
# app config
|
||||
app_config = AppConfig(
|
||||
datapath=datapath,
|
||||
dataroot=dataroot,
|
||||
title=title,
|
||||
about=about,
|
||||
scripts=scripts,
|
||||
layout=embedding,
|
||||
max_category_items=max_category_items,
|
||||
diffexp_lfc_cutoff=diffexp_lfc_cutoff,
|
||||
obs_names=obs_names,
|
||||
var_names=var_names,
|
||||
anndata_backed=backed,
|
||||
disable_diffexp=disable_diffexp)
|
||||
|
||||
server.create_app()
|
||||
server.app.config.update(SCRIPTS=scripts)
|
||||
matrix_data_cache_manager = MatrixDataCacheManager()
|
||||
data_adaptor = None
|
||||
if datapath:
|
||||
try:
|
||||
with matrix_data_cache_manager.data_adaptor(datapath, app_config) as data_adaptor:
|
||||
if not disable_diffexp and data_adaptor.parameters.get("diffexp_may_be_slow", False):
|
||||
click.echo(
|
||||
f"[cellxgene] CAUTION: due to the size of your dataset, "
|
||||
f"running differential expression may take longer or fail."
|
||||
)
|
||||
except Exception as e:
|
||||
raise click.ClickException(str(e))
|
||||
|
||||
# create an annotations object. Only AnnotationsLocalFile is used (for now)
|
||||
annotations = None
|
||||
|
||||
if experimental_annotations:
|
||||
annotations = AnnotationsLocalFile(experimental_annotations_output_dir,
|
||||
experimental_annotations_file)
|
||||
|
||||
# if the user has specified a fixed label file, go ahead and validate it
|
||||
# so that we can remove errors early in the process.
|
||||
|
||||
if experimental_annotations_file and data_adaptor:
|
||||
data_adaptor.check_new_labels(annotations.read_labels(data_adaptor))
|
||||
|
||||
if experimental_annotations_ontology or bool(experimental_annotations_ontology_obo):
|
||||
try:
|
||||
annotations.load_ontology(experimental_annotations_ontology_obo)
|
||||
except OntologyLoadFailure as e:
|
||||
raise click.ClickException("Unable to load ontology terms\n" + str(e))
|
||||
|
||||
# create the server
|
||||
from server.app.app import Server
|
||||
server = Server(matrix_data_cache_manager, annotations, app_config)
|
||||
|
||||
if not verbose:
|
||||
log = logging.getLogger("werkzeug")
|
||||
log.setLevel(logging.ERROR)
|
||||
|
||||
file_size = data_locator.size() if data_locator.islocal() else 0
|
||||
|
||||
# if a big file, let the user know it may take a while to load.
|
||||
if file_size > BIG_FILE_SIZE_THRESHOLD:
|
||||
click.echo(f"[cellxgene] Loading data from {basename(data)}, this may take a while...")
|
||||
else:
|
||||
click.echo(f"[cellxgene] Loading data from {basename(data)}.")
|
||||
|
||||
from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
|
||||
|
||||
try:
|
||||
server.attach_data(ScanpyEngine(data_locator, e_args), title=title, about=about)
|
||||
except ScanpyFileError as e:
|
||||
raise click.ClickException(f"{e}")
|
||||
|
||||
if not disable_diffexp and server.app.data.config["diffexp_may_be_slow"]:
|
||||
click.echo(
|
||||
f"[cellxgene] CAUTION: due to the size of your dataset, "
|
||||
f"running differential expression may take longer or fail."
|
||||
)
|
||||
|
||||
if open_browser:
|
||||
click.echo(f"[cellxgene] Launching! Opening your browser to {cellxgene_url} now.")
|
||||
webbrowser.open(cellxgene_url)
|
||||
|
||||
@@ -4,7 +4,7 @@ import click
|
||||
from numpy import ndarray, unique
|
||||
from scipy.sparse.csc import csc_matrix
|
||||
|
||||
from server.utils.utils import sort_options
|
||||
from server.common.utils import sort_options
|
||||
|
||||
|
||||
@sort_options
|
||||
|
||||
Reference in New Issue
Block a user