Refactoring cxg utility classes in preparation for CXG conversion tooling (#1739)

server/cli/launch.py

@@ -1,19 +1,19 @@
 import errno
 import functools
 import logging
-from os import devnull
 import sys
 import webbrowser
+from os import devnull
 
 import click
 from flask_compress import Compress
 from flask_cors import CORS
 
-from server.common.utils import sort_options
-from server.common.errors import DatasetAccessError, ConfigurationError
+from server.app.app import Server
 from server.common.app_config import AppConfig
 from server.common.default_config import default_config
-from server.app.app import Server
+from server.common.errors import DatasetAccessError, ConfigurationError
+from server.common.utils.utils import sort_options
 
 DEFAULT_CONFIG = AppConfig()
 
@@ -33,7 +33,7 @@ def annotation_args(func):
         multiple=False,
         metavar="<path>",
         help="CSV file to initialize editing of existing annotations; will be altered in-place. "
-        "Incompatible with --annotations-dir.",
+             "Incompatible with --annotations-dir.",
     )
     @click.option(
         "--annotations-dir",
@@ -42,7 +42,7 @@ def annotation_args(func):
         multiple=False,
         metavar="<directory path>",
         help="Directory of where to save output annotations; filename will be specified in the application. "
-        "Incompatible with --annotations-file.",
+             "Incompatible with --annotations-file.",
     )
     @click.option(
         "--experimental-annotations-ontology",
@@ -170,7 +170,7 @@ def server_args(func):
         default=DEFAULT_CONFIG.server_config.app__debug,
         show_default=True,
         help="Run in debug mode. This is helpful for cellxgene developers, "
-        "or when you want more information about an error condition.",
+             "or when you want more information about an error condition.",
     )
     @click.option(
         "--verbose",
@@ -203,7 +203,7 @@ def server_args(func):
         multiple=True,
         metavar="<text>",
         help="Additional script files to include in HTML page. If not specified, "
-        "no additional script files will be included.",
+             "no additional script files will be included.",
         show_default=False,
     )
     @functools.wraps(func)
@@ -223,7 +223,7 @@ def launch_args(func):
         default=DEFAULT_CONFIG.server_config.multi_dataset__dataroot,
         metavar="<data directory>",
         help="Enable cellxgene to serve multiple files. Supply path (local directory or URL)"
-        " to folder containing H5AD and/or CXG datasets.",
+             " to folder containing H5AD and/or CXG datasets.",
         hidden=True,
     )  # TODO, unhide when dataroot is supported)
     @click.argument("datapath", required=False, metavar="<path to data file>")
@@ -307,32 +307,32 @@ class CliLaunchServer(Server):
 )
 @launch_args
 def launch(
-    datapath,
-    dataroot,
-    verbose,
-    debug,
-    open_browser,
-    port,
-    host,
-    embedding,
-    obs_names,
-    var_names,
-    max_category_items,
-    disable_custom_colors,
-    diffexp_lfc_cutoff,
-    title,
-    scripts,
-    about,
-    disable_annotations,
-    annotations_file,
-    annotations_dir,
-    backed,
-    disable_diffexp,
-    experimental_annotations_ontology,
-    experimental_annotations_ontology_obo,
-    experimental_enable_reembedding,
-    config_file,
-    dump_default_config,
+        datapath,
+        dataroot,
+        verbose,
+        debug,
+        open_browser,
+        port,
+        host,
+        embedding,
+        obs_names,
+        var_names,
+        max_category_items,
+        disable_custom_colors,
+        diffexp_lfc_cutoff,
+        title,
+        scripts,
+        about,
+        disable_annotations,
+        annotations_file,
+        annotations_dir,
+        backed,
+        disable_diffexp,
+        experimental_annotations_ontology,
+        experimental_annotations_ontology_obo,
+        experimental_enable_reembedding,
+        config_file,
+        dump_default_config,
 ):
     """Launch the cellxgene data viewer.
     This web app lets you explore single-cell expression data.

server/cli/prepare.py

@@ -5,7 +5,7 @@ import pandas as pd
 from numpy import ndarray, unique
 from scipy.sparse.csc import csc_matrix
 
-from server.common.utils import sort_options
+from server.common.utils.utils import sort_options
 
 
 @sort_options
@@ -37,7 +37,7 @@ from server.common.utils import sort_options
     default=False,
     is_flag=True,
     help="Do not run quality control metrics. By default cellxgene runs them "
-    "(saved to adata.obs and adata.var; see scanpy.pp.calculate_qc_metrics for details).",
+         "(saved to adata.obs and adata.var; see scanpy.pp.calculate_qc_metrics for details).",
 )
 @click.option(
     "--make-obs-names-unique/--no-make-obs-names-unique",
@@ -53,18 +53,18 @@ from server.common.utils import sort_options
 )
 @click.help_option("--help", "-h", help="Show this message and exit.")
 def prepare(
-    data,
-    embedding,
-    recipe,
-    output,
-    plotting,
-    sparse,
-    overwrite,
-    set_obs_names,
-    set_var_names,
-    skip_qc,
-    make_obs_names_unique,
-    make_var_names_unique,
+        data,
+        embedding,
+        recipe,
+        output,
+        plotting,
+        sparse,
+        overwrite,
+        set_obs_names,
+        set_var_names,
+        skip_qc,
+        make_obs_names_unique,
+        make_var_names_unique,
 ):
     """
     Preprocess data for use with cellxgene.