fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-09-24 07:08:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

annotations cli updates (#1190)

Browse Source 
* 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
2020-03-11 11:57:52 -07:00
committed by GitHub
co-authored by Matt Weiden
parent 8beeb57c96
commit 9089fc98f2
7 changed files with 50 additions and 55 deletions
Download Patch File Download Diff File Expand all files Collapse all files
server/cli/launch.py
+27 -27
View File
@@ -26,29 +26,29 @@ DEFAULT_SERVER_PORT = int(environ.get("CXG_SERVER_PORT", "5005"))
def annotation_args(func):
@click.option(
"--experimental-annotations",
"--disable-annotations",
is_flag=True,
default=False,
show_default=True,
help="Enable user annotation of data.",
help="Disable user annotation of data.",
)
@click.option(
"--experimental-annotations-file",
"--annotations-file",
default=None,
show_default=True,
multiple=False,
metavar="<path>",
help="CSV file to initialize editing of existing annotations; will be altered in-place. "
"Incompatible with --annotations-output-dir.",
"Incompatible with --annotations-dir.",
)
@click.option(
"--experimental-annotations-output-dir",
"--annotations-dir",
default=None,
show_default=False,
multiple=False,
metavar="<directory path>",
help="Directory of where to save output annotations; filename will be specified in the application. "
"Incompatible with --annotations-input-file.",
"Incompatible with --annotations-file.",
)
@click.option(
"--experimental-annotations-ontology",
@@ -279,9 +279,9 @@ def launch(
title,
scripts,
about,
experimental_annotations,
experimental_annotations_file,
experimental_annotations_output_dir,
disable_annotations,
annotations_file,
annotations_dir,
backed,
disable_diffexp,
experimental_annotations_ontology,
@@ -359,32 +359,32 @@ def launch(
else:
port = find_available_port(host, DEFAULT_SERVER_PORT)
if not experimental_annotations:
if experimental_annotations_file is not None:
click.echo("Warning: --experimental-annotations-file ignored as --annotations not enabled.")
if experimental_annotations_output_dir is not None:
click.echo("Warning: --experimental-annotations-output-dir ignored as --annotations not enabled.")
if disable_annotations:
if annotations_file is not None:
click.echo("Warning: --annotations-file ignored as annotations are disabled.")
if annotations_dir is not None:
click.echo("Warning: --annotations-dir ignored as annotations are disabled.")
if experimental_annotations_ontology:
click.echo("Warning: --experimental-annotations-ontology ignored as --annotations not enabled.")
click.echo("Warning: --experimental-annotations-ontology ignored as annotations are disabled.")
if experimental_annotations_ontology_obo is not None:
click.echo("Warning: --experimental-annotations-ontology-obo ignored as --annotations not enabled.")
click.echo("Warning: --experimental-annotations-ontology-obo ignored as annotations are disabled.")
else:
if experimental_annotations_file is not None and experimental_annotations_output_dir is not None:
if annotations_file is not None and annotations_dir is not None:
raise click.ClickException(
"--experimental-annotations-file and --experimental-annotations-output-dir " "may not be used together."
"--annotations-file and --annotations-dir " "may not be used together."
)
if experimental_annotations_file is not None:
lf_name, lf_ext = splitext(experimental_annotations_file)
if annotations_file is not None:
lf_name, lf_ext = splitext(annotations_file)
if lf_ext and lf_ext != ".csv":
raise click.FileError(basename(experimental_annotations_file), hint="annotation file type must be .csv")
raise click.FileError(basename(annotations_file), hint="annotation file type must be .csv")
if experimental_annotations_output_dir is not None and not isdir(experimental_annotations_output_dir):
if annotations_dir is not None and not isdir(annotations_dir):
try:
mkdir(experimental_annotations_output_dir)
mkdir(annotations_dir)
except OSError:
raise click.ClickException(
"Unable to create directory specified by " "--experimental-annotations-output-dir"
"Unable to create directory specified by " "--annotations-dir"
)
if about:
@@ -438,13 +438,13 @@ def launch(
# 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 not disable_annotations:
annotations = AnnotationsLocalFile(annotations_dir, 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:
if 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):