Refactor czi_hosted and server into backend directory, pull common code into backend/common, refactor tests (#2102)

* move local_server -> backend/server server-> backend/czi_hosted, pull common code into backend/common update imports, tests and make commands
2026-09-27 07:18:12 +08:00 · 2021-03-26 00:27:07 -05:00
parent e6e358ddc8
commit 78c9d24ed4
425 changed files with 734 additions and 5317 deletions
@@ -1,118 +0,0 @@
-import contextlib
-import errno
-import importlib.util
-import logging
-import os
-import pkgutil
-import socket
-from urllib.parse import urlsplit, urljoin
-
-import numpy as np
-from flask import json
-
-from server.common.errors import ConfigurationError
-
-
-def find_available_port(host, port=5005):
-    """
-    Helper method to find open port on host. Tries 5000 ports incremented from the specified port
-    """
-    # Takes approx 2 seconds to do a scan of 5000 ports on my laptop
-    num_ports_to_try = 5000
-    for port_to_try in range(port, port + num_ports_to_try):
-        if is_port_available(host, port_to_try):
-            return port_to_try
-    raise socket.error(errno.EADDRINUSE, f"No port in range {port} - {port + num_ports_to_try - 1} available.")
-
-
-def is_port_available(host, port):
-    is_available = False
-    with contextlib.closing(socket.socket(socket.AF_INET, socket.SOCK_STREAM)) as s:
-        try:
-            s.bind((host, port))
-            is_available = True
-        except socket.error:
-            pass
-    return is_available
-
-
-def sort_options(command):
-    """
-    Helper for the click options - will sort options in a command, and can
-    be used as a decorator.
-    """
-    command.params.sort(key=lambda p: p.name)
-    return command
-
-
-def path_join(base, *urls):
-    """
-    this is like urllib.parse.urljoin, except it works around the scheme-specific
-    cleverness in the aforementioned code, ignores anything in the url except the path,
-    and accepts more than one url.
-    """
-    if not base.endswith("/"):
-        base += "/"
-    btpl = urlsplit(base)
-    path = btpl.path
-    for url in urls:
-        utpl = urlsplit(url)
-        if btpl.scheme == "":
-            path = os.path.join(path, utpl.path)
-            path = os.path.normpath(path)
-        else:
-            path = urljoin(path, utpl.path)
-    return btpl._replace(path=path).geturl()
-
-
-class Float32JSONEncoder(json.JSONEncoder):
-    def __init__(self, *args, **kwargs):
-        """
-        NaN/Infinities are illegal in standard JSON.  Python extends JSON with
-        non-standard symbols that most JavaScript JSON parsers do not understand.
-        The `allow_nan` parameter will force Python simplejson to throw an ValueError
-        if it runs into non-finite floating point values which are unsupported by
-        standard JSON.
-        """
-        kwargs["allow_nan"] = False
-        super().__init__(*args, **kwargs)
-
-    def default(self, obj):
-        if isinstance(obj, np.float32):
-            return float(obj)
-        elif isinstance(obj, np.integer):
-            return int(obj)
-        return json.JSONEncoder.default(self, obj)
-
-
-def custom_format_warning(msg, *args, **kwargs):
-    return f"[cellxgene] Warning: {msg} \n"
-
-
-def jsonify_numpy(data):
-    return json.dumps(data, cls=Float32JSONEncoder, allow_nan=False)
-
-
-def import_plugins(plugin_module):
-    """
-    Load optional plugin modules from server.common.plugins
-
-    If you would like to customize cellxgene, you can add submodules to server.common.plugins before running the app.
-    This code will import each, loading the code in each. If no plugins are defined, initializing the app continues as
-    normal.
-    """
-    loaded_modules = []
-    try:
-        pkg = importlib.import_module(plugin_module)
-        for loader, name, is_pkg in pkgutil.walk_packages(pkg.__path__):
-            full_name = f"{plugin_module}.{name}"
-            try:
-                module = importlib.import_module(full_name)
-            except Exception as e:
-                raise ConfigurationError(f"Unexpected error while importing plugin: {plugin_module}.{name}: {str(e)}")
-            loaded_modules.append(module)
-    except ModuleNotFoundError as e:
-        #  This exception occurs when the plugin_module does not exist (not an error).
-        logging.debug(f"No plugins found in module: {plugin_module}: {str(e)}")
-
-    return loaded_modules