CLI refactor (#396)

* refactor cli to improve ux and enable easy incorporation of prepare as a subcommand

* switches to use click, which removes some boilerplate and gets us some improved ux for free

* changes the entry point for the cli

* changes the name of the browser option to --open and makes the default false

.travis.yml

@@ -14,6 +14,7 @@ install:
 script:
   - set -eo pipefail
   - flake8 server/app/
+  - flake8 server/cli/
   - npm run --prefix client/ build
   - npm run --prefix client/ test
   - pytest -s server/test

server/__main__.py

@@ -8,5 +8,5 @@ if __package__ is None:
     __package__ = PKG_PATH.name
 
 # Main thing
-from .app.app import main
-main()
+from .cli.cli import cli
+cli()

server/app/app.py

@@ -1,8 +1,4 @@
-import argparse
-import logging
 import os
-import sys
-import webbrowser
 
 from flask import Flask
 from flask_caching import Cache
@@ -11,7 +7,7 @@ from flask_cors import CORS
 from flask_restful_swagger_2 import get_swagger_blueprint
 
 from .rest_api.rest import get_api_resources
-from .util.utils import Float32JSONEncoder, whole_number
+from .util.utils import Float32JSONEncoder
 from .web import webapp
 
 REACTIVE_LIMIT = 1_000_000
@@ -32,7 +28,6 @@ app.config.update(
 # Application Data
 data = None
 
-
 # A list of swagger document objects
 docs = []
 resources = get_api_resources()
@@ -45,121 +40,3 @@ app.register_blueprint(
                           description="An API connecting ExpressionMatrix2 clustering algorithm to cellxgene"))
 
 app.add_url_rule("/", endpoint="index")
-
-
-def create_cli():
-    parser = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter)
-    parser.description = """
-synopsis:
-cellxgene <command> <data> [options]
-
-description:
-
-cellxgene is a local web application for exploring single cell expression.
-    """
-    parser.add_argument("-V", "--version", help="show version and exit")
-    subparsers = parser.add_subparsers(dest="command")
-    subparsers.required = True
-    launch_group = subparsers.add_parser("launch", help="launch web application",
-                                         formatter_class=argparse.RawTextHelpFormatter)
-    launch_group.description = """
-    cellxgene launches a local web application for exploring single cell expression data.
-
-    Data must be in a format that cellxgene expects [[ how to format ]]
-
-    examples:
-    To run with the example dataset:
-
-        cellxgene example_dataset/pbmc3k.h5ad --title PBMC3K
-
-    To run with your own data with tsne layout:
-
-        cellxgene <your data file> --title <your title> -l tsne
-
-    To indicate that the human-readable variable annotation is named 'gene_names', and the human-readable observation
-    is 'cell_names':
-
-        cellxgene mydata.h5ad -var-name gene_names -obs-name cell_names
-        """
-    launch_group.epilog = """
-    annotation names:
-    The data viewer requires a unique, human readable name for each observation and variable.  These are used for
-    various application features, such as the ability to view expression by gene. When launching cellxgene, appropriate
-    observation and variable annotations must be identified.
-
-    If --obs-name or --var-name parameters are specified, values in the named annotations will be used. If not
-    specified, the observation and variable index values will name each respectively.  An error will generated if the
-    values for each are not unique.
-        """
-    launch_group.add_argument("data", metavar="data", help="file containing the data to display")
-    launch_group.add_argument("--title", "-t", help="title to display -- if this is omitted the title will be the name "
-                                                    "of the data file.")
-    launch_group.add_argument(
-        "--listen-all",
-        help="bind to all interfaces (this makes the server accessible beyond this computer)",
-        action="store_true")
-    launch_group.add_argument("--port", help="port to run server on", type=int, default=5005)
-    launch_group.add_argument("-v", "--verbose", action="store_true",
-                              help="more verbose output, including outputting warnings and every REST request")
-    launch_group.add_argument("--debug", action="store_true", help=argparse.SUPPRESS)
-    launch_group.add_argument("--no-open", help="do not launch the webbrowser", action="store_false",
-                              dest="open_browser")
-    launch_group.add_argument("--obs-names", help="Annotation name to use as unique, human-readable observation name")
-    launch_group.add_argument("--var-names", help="Annotation name to use as unique, human-readable variable name")
-    launch_group.add_argument(
-        "--max-category-items",
-        type=whole_number,
-        help="Limit for the cardinality of a categorical annotation, beyond which the"
-             " annotation will not be available for user selection in the front-end",
-        default=100)
-    # TODO scanpy specific; rethink when we add another engine
-    computation_group = launch_group.add_argument_group('computational arguments')
-    # TODO these choices should be generated from the actual available methods see GH issue #94
-    computation_group.add_argument("-l", "--layout", choices=["umap", "tsne"], default="umap",
-                                   help="Algorithm to use for graph layout")
-    computation_group.add_argument("-d", "--diffexp", choices=["ttest"], default="ttest",
-                                   help="Algorithm to used to calculate differential expression")
-    return parser
-
-
-def run_scanpy(args):
-    title = args.title
-    if not title:
-        file_parts = os.path.splitext(os.path.basename(args.data))
-        title = file_parts[0]
-    if args.listen_all:
-        host = "0.0.0.0"
-    else:
-        host = "127.0.0.1"
-    cellxgene_url = f"http://{host}:{args.port}"
-    api_base = f"{cellxgene_url}/api/"
-    app.config.update(
-        DATASET_TITLE=title,
-        CXG_API_BASE=api_base
-    )
-
-    if not args.verbose:
-        log = logging.getLogger('werkzeug')
-        log.setLevel(logging.ERROR)
-    from .scanpy_engine.scanpy_engine import ScanpyEngine
-    print(f"Loading data from {args.data} (this may take a while)")
-    app.data = ScanpyEngine(args.data, args)
-    print(f"Launching cellxgene")
-    if args.open_browser:
-        webbrowser.open(cellxgene_url)
-    print(f"Please go to {cellxgene_url}")
-    app.run(host=host, debug=args.debug, port=args.port)
-
-
-def main():
-    parser = create_cli()
-    args = parser.parse_args()
-    # Debug sets up developer mode
-    if args.debug:
-        args.verbose = True
-        args.open_browser = False
-    if not args.verbose:
-        sys.tracebacklimit = 0
-    # TODO pick engine based on input file
-    print("cellxgene starting...\n")
-    run_scanpy(args)

server/app/driver/driver.py

@@ -14,9 +14,9 @@ class CXGDriver(metaclass=ABCMeta):
 
     def __init__(self, data, args):
         self.data = self._load_data(data)
-        self.layout_method = args.layout
-        self.diffexp_method = args.diffexp
-        self.max_category_items = args.max_category_items
+        self.layout_method = args['layout']
+        self.diffexp_method = args['diffexp']
+        self.max_category_items = args['max_category_items']
         self.cluster = None
 
     @property

server/app/scanpy_engine/scanpy_engine.py

@@ -24,8 +24,8 @@ class ScanpyEngine(CXGDriver):
 
     def __init__(self, data, args):
         super().__init__(data, args)
-        self._alias_annotation_names(Axis.OBS, args.obs_names)
-        self._alias_annotation_names(Axis.VAR, args.var_names)
+        self._alias_annotation_names(Axis.OBS, args['obs_names'])
+        self._alias_annotation_names(Axis.VAR, args['var_names'])
         self._validate_data_types()
         self.cell_count = self.data.shape[0]
         self.gene_count = self.data.shape[1]

server/cli/cli.py

@@ -0,0 +1,12 @@
+import click
+
+from .launch import launch
+
+
+@click.group(name='cellxgene', context_settings=dict(max_content_width=85))
+@click.version_option(version='0.0.1', prog_name='cellxgene', message='[%(prog)s] Version %(version)s')
+def cli():
+    pass
+
+
+cli.add_command(launch)

server/cli/launch.py

@@ -0,0 +1,99 @@
+import sys
+import click
+import logging
+import webbrowser
+
+from os.path import splitext, basename
+
+
+@click.command()
+@click.argument('data', metavar='<data file>', type=click.Path(exists=True, file_okay=True, dir_okay=False))
+@click.option('--layout', '-l', type=click.Choice(['umap', 'tsne']), default='umap', show_default=True,
+              help='Method for layout.')
+@click.option('--diffexp', '-d', type=click.Choice(['ttest']), default='ttest', show_default=True,
+              help='Method for differential expression.')
+@click.option('--title', '-t', help='Title to display (if omitted will use file name).', metavar='')
+@click.option('--verbose', '-v', is_flag=True, default=False, show_default=True,
+              help='Provide verbose output, including warnings and all server requests.')
+@click.option('--debug', '-d', is_flag=True, default=False, show_default=True,
+              help='Run in debug mode.')
+@click.option('--open', '-o', 'open_browser', is_flag=True, default=False, show_default=True,
+              help='Open the web browser after launch.')
+@click.option('--port', '-p', help="Port to run server on.", metavar='', default=5005, show_default=True)
+@click.option('--obs-names', default=None, metavar='', help='Name of annotation field to use for observations.')
+@click.option('--var-names', default=None, metavar='', help='Name of annotation to use for variables.')
+@click.option('--listen-all', is_flag=True, default=False, show_default=True,
+              help='Bind to all interfaces (this makes the server accessible beyond this computer).')
+@click.option('--max-category-items', default=100, metavar='', show_default=True,
+              help='Limits the number of categorical annotation items displayed.')
+def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
+           open_browser, port, listen_all, max_category_items):
+    """Launch the cellxgene data viewer.
+    This web app lets you explore single-cell expression data.
+    Data must be in a format that cellxgene expects, read the
+    "getting started" guide.
+
+    Examples:
+
+    > cellxgene launch example_dataset/pbmc3k.h5ad --title pbmc3k
+
+    > cellxgene launch <your data file> --title <your title>"""
+
+    # Startup message
+    click.echo('[cellxgene] Starting the CLI...')
+
+    # Import Flask app
+    from server.app.app import app
+
+    # Argument checking
+    name, extension = splitext(data)
+    if extension != '.h5ad':
+        raise click.FileError(basename(data), hint='file type must be .h5ad')
+
+    if debug:
+        verbose = True
+        open_browser = False
+
+    if not verbose:
+        sys.tracebacklimit = 0
+
+    if not title:
+        file_parts = splitext(basename(data))
+        title = file_parts[0]
+
+    if listen_all:
+        host = '0.0.0.0'
+    else:
+        host = '127.0.0.1'
+
+    # Setup app
+    cellxgene_url = f"http://{host}:{port}"
+    api_base = f"{cellxgene_url}/api/"
+
+    app.config.update(
+        DATASET_TITLE=title,
+        CXG_API_BASE=api_base
+        )
+
+    if not verbose:
+        log = logging.getLogger('werkzeug')
+        log.setLevel(logging.ERROR)
+
+    click.echo(f'[cellxgene] Loading data from {basename(data)}, this may take awhile...')
+
+    from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
+
+    args = {'layout': layout, 'diffexp': diffexp, 'max_category_items': max_category_items,
+            'obs_names': obs_names, 'var_names': var_names}
+
+    app.data = ScanpyEngine(data, args)
+
+    if open_browser:
+        click.echo(f'[cellxgene] Launching! Opening your browser to {cellxgene_url} now.')
+        webbrowser.open(cellxgene_url)
+    else:
+        click.echo(f'[cellxgene] Launching! Please go to {cellxgene_url} in your browser.')
+
+    click.echo('[cellxgene] Type CTRL-C at any time to exit.')
+
+    app.run(host=host, debug=debug, port=port)

server/test/test_api.py

@@ -25,7 +25,7 @@ class EndPoints(unittest.TestCase):
 
     @classmethod
     def setUpClass(cls):
-        cls.ps = Popen(["cellxgene", "launch", "--no-open", "example-dataset/pbmc3k.h5ad"])
+        cls.ps = Popen(["cellxgene", "launch", "example-dataset/pbmc3k.h5ad", "--debug"])
         session = requests.Session()
         for i in range(90):
             try:

server/test/test_scanpy_engine.py

@@ -13,12 +13,8 @@ from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
 
 class UtilTest(unittest.TestCase):
     def setUp(self):
-        args = argparse.Namespace()
-        args.layout = "umap"
-        args.diffexp = "ttest"
-        args.max_category_items = 100
-        args.obs_names = None
-        args.var_names = None
+        args = {'layout': 'umap', 'diffexp': 'ttest', 'max_category_items': 100,
+                'obs_names': None, 'var_names': None}
 
         self.data = ScanpyEngine("example-dataset/pbmc3k.h5ad", args)
         self.data._create_schema()

setup.py

@@ -25,6 +25,6 @@ setup(
     ),
     entry_points={
         "console_scripts":
-            ["cellxgene = server.app.app:main"]
+            ["cellxgene = server.cli.cli:cli"]
     }
 )