mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-27 12:08:11 +08:00
annotations cli updates (#1190)
* Switch logic from `--annotations` to `--disable-annotations * Rename `--annotations-file` --> `--annotations-input-file` and remove `experimental` * update docs * update makefile * update tests * Disable annotations on standard client smoke test * Update docs/posts/annotations.md Co-Authored-By: Matt Weiden <538456+mweiden@users.noreply.github.com> * Update docs/posts/annotations.md * Renaming * Docs * Update tests * Pesky typo -_- Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
This commit is contained in:
Sidney Bell
co-authored by
Matt Weiden
Matt Weiden
parent
8beeb57c96
commit
9089fc98f2
+27
-27
@@ -26,29 +26,29 @@ DEFAULT_SERVER_PORT = int(environ.get("CXG_SERVER_PORT", "5005"))
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def annotation_args(func):
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@click.option(
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"--experimental-annotations",
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"--disable-annotations",
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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="Enable user annotation of data.",
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help="Disable user annotation of data.",
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)
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@click.option(
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"--experimental-annotations-file",
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"--annotations-file",
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default=None,
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show_default=True,
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multiple=False,
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metavar="<path>",
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help="CSV file to initialize editing of existing annotations; will be altered in-place. "
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"Incompatible with --annotations-output-dir.",
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"Incompatible with --annotations-dir.",
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)
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@click.option(
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"--experimental-annotations-output-dir",
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"--annotations-dir",
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default=None,
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show_default=False,
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multiple=False,
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metavar="<directory path>",
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help="Directory of where to save output annotations; filename will be specified in the application. "
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"Incompatible with --annotations-input-file.",
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"Incompatible with --annotations-file.",
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)
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@click.option(
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"--experimental-annotations-ontology",
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@@ -279,9 +279,9 @@ def launch(
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title,
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scripts,
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about,
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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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disable_annotations,
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annotations_file,
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annotations_dir,
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backed,
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disable_diffexp,
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experimental_annotations_ontology,
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@@ -359,32 +359,32 @@ def launch(
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else:
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port = find_available_port(host, DEFAULT_SERVER_PORT)
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if not experimental_annotations:
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if experimental_annotations_file is not None:
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click.echo("Warning: --experimental-annotations-file ignored as --annotations not enabled.")
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if experimental_annotations_output_dir is not None:
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click.echo("Warning: --experimental-annotations-output-dir ignored as --annotations not enabled.")
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if disable_annotations:
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if annotations_file is not None:
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click.echo("Warning: --annotations-file ignored as annotations are disabled.")
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if annotations_dir is not None:
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click.echo("Warning: --annotations-dir ignored as annotations are disabled.")
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if experimental_annotations_ontology:
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click.echo("Warning: --experimental-annotations-ontology ignored as --annotations not enabled.")
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click.echo("Warning: --experimental-annotations-ontology ignored as annotations are disabled.")
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if experimental_annotations_ontology_obo is not None:
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click.echo("Warning: --experimental-annotations-ontology-obo ignored as --annotations not enabled.")
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click.echo("Warning: --experimental-annotations-ontology-obo ignored as annotations are disabled.")
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else:
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if experimental_annotations_file is not None and experimental_annotations_output_dir is not None:
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if annotations_file is not None and annotations_dir is not None:
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raise click.ClickException(
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"--experimental-annotations-file and --experimental-annotations-output-dir " "may not be used together."
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"--annotations-file and --annotations-dir " "may not be used together."
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)
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if experimental_annotations_file is not None:
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lf_name, lf_ext = splitext(experimental_annotations_file)
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if annotations_file is not None:
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lf_name, lf_ext = splitext(annotations_file)
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if lf_ext and lf_ext != ".csv":
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raise click.FileError(basename(experimental_annotations_file), hint="annotation file type must be .csv")
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raise click.FileError(basename(annotations_file), hint="annotation file type must be .csv")
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if experimental_annotations_output_dir is not None and not isdir(experimental_annotations_output_dir):
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if annotations_dir is not None and not isdir(annotations_dir):
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try:
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mkdir(experimental_annotations_output_dir)
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mkdir(annotations_dir)
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except OSError:
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raise click.ClickException(
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"Unable to create directory specified by " "--experimental-annotations-output-dir"
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"Unable to create directory specified by " "--annotations-dir"
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)
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if about:
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@@ -438,13 +438,13 @@ def launch(
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# create an annotations object. Only AnnotationsLocalFile is used (for now)
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annotations = None
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if experimental_annotations:
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annotations = AnnotationsLocalFile(experimental_annotations_output_dir, experimental_annotations_file)
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if not disable_annotations:
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annotations = AnnotationsLocalFile(annotations_dir, annotations_file)
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# if the user has specified a fixed label file, go ahead and validate it
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# so that we can remove errors early in the process.
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if experimental_annotations_file and data_adaptor:
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if annotations_file and data_adaptor:
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data_adaptor.check_new_labels(annotations.read_labels(data_adaptor))
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if experimental_annotations_ontology or bool(experimental_annotations_ontology_obo):
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@@ -110,7 +110,7 @@ class AppConfig(object):
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"enable-reembedding": self.enable_reembedding,
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"annotations": False,
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"annotations_file": None,
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"annotations_output_dir": 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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@@ -17,7 +17,7 @@ BAD_FILTER = {"filter": {"obs": {"annotation_value": [{"name": "xyz"}]}}}
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class EndPoints(object):
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ANNOTATIONS_ENABLED = False
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ANNOTATIONS_ENABLED = True
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def setUp(self):
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self.session = requests.Session()
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@@ -324,6 +324,7 @@ class EndPointsAnndata(unittest.TestCase, EndPoints):
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LOCAL_URL = f"http://127.0.0.1:{PORT}/"
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VERSION = "v0.2"
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URL_BASE = f"{LOCAL_URL}api/{VERSION}/"
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ANNOTATIONS_ENABLED = False
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@classmethod
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def setUpClass(cls):
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@@ -334,6 +335,7 @@ class EndPointsAnndata(unittest.TestCase, EndPoints):
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"--no-upgrade-check",
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"launch",
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"../example-dataset/pbmc3k.h5ad",
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"--disable-annotations",
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"--verbose",
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"--port",
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str(cls.PORT),
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@@ -356,6 +358,7 @@ class EndPointsCxg(unittest.TestCase, EndPoints):
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LOCAL_URL = f"http://127.0.0.1:{PORT}/"
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VERSION = "v0.2"
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URL_BASE = f"{LOCAL_URL}api/{VERSION}/"
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ANNOTATIONS_ENABLED = False
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@classmethod
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def setUpClass(cls):
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@@ -366,6 +369,7 @@ class EndPointsCxg(unittest.TestCase, EndPoints):
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"--no-upgrade-check",
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"launch",
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"test/test_datasets/pbmc3k.cxg",
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"--disable-annotations",
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"--verbose",
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"--port",
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str(cls.PORT),
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@@ -398,8 +402,7 @@ class EndPointsAnndataAnnotations(unittest.TestCase, EndPointsAnnotations):
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"cellxgene",
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"--no-upgrade-check",
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"launch",
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"--experimental-annotations",
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"--experimental-annotations-file",
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"--annotations-file",
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cls.annotations.output_file,
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"--verbose",
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"--port",
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@@ -433,8 +436,7 @@ class EndPointsCxgAnnotations(unittest.TestCase, EndPointsAnnotations):
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"cellxgene",
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"--no-upgrade-check",
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"launch",
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"--experimental-annotations",
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"--experimental-annotations-file",
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"--annotations-file",
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cls.annotations.output_file,
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"--verbose",
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"--port",
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