port retry (#761)

* WIP

* import find_available_port method

* move method to utils

so I can add to eventually add to gui

* add fixed-port flag to tests

* Update server/utils/utils.py

Co-Authored-By: Tony Tung <tonytung@merly.org>

* pr review suggestions

* pr review suggestions

* fix outdated package.json

* update error message

* simplify find_available_port function

* Auto scan for ports unless port is specified.

* fix tests

* fix comment for find_available_port

* lint error

* differentiate port error from generic os error

* add errno to OSerror

* pr review fixes

* raise e -> raise

* oserror -> socket error

server/cli/launch.py

@@ -1,3 +1,4 @@
+import errno
 import logging
 from os import devnull
 from os.path import splitext, basename, getsize
@@ -12,6 +13,7 @@ from server.app.app import Server
 from server.app.util.errors import ScanpyFileError
 from server.app.util.utils import custom_format_warning
 from server.utils.constants import MODES
+from server.utils.utils import find_available_port
 
 
 # anything bigger than this will generate a special message
@@ -55,7 +57,8 @@ BIG_FILE_SIZE_THRESHOLD = 100 * 2**20  # 100MB
     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("--port", "-p", help="Port to run server on, if not specified cellxgene will find an available port.",
+              metavar="", 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("--host", default="127.0.0.1", help="Host IP address")
@@ -140,6 +143,9 @@ security risk by including the --scripts flag. Make sure you trust the scripts t
         file_parts = splitext(basename(data))
         title = file_parts[0]
 
+    if not port:
+        port = find_available_port(host)
+
     # Setup app
     cellxgene_url = f"http://{host}:{port}"
 
@@ -197,4 +203,9 @@ security risk by including the --scripts flag. Make sure you trust the scripts t
         f = open(devnull, "w")
         sys.stdout = f
 
-    server.app.run(host=host, debug=debug, port=port, threaded=True)
+    try:
+        server.app.run(host=host, debug=debug, port=port, threaded=True)
+    except OSError as e:
+        if e.errno == errno.EADDRINUSE:
+            raise click.ClickException("Port is in use, please specify an open port using the --port flag.") from e
+        raise

server/test/test_api.py

@@ -19,7 +19,7 @@ class EndPoints(unittest.TestCase):
 
     @classmethod
     def setUpClass(cls):
-        cls.ps = Popen(["cellxgene", "launch", "example-dataset/pbmc3k.h5ad", "--debug"])
+        cls.ps = Popen(["cellxgene", "launch", "example-dataset/pbmc3k.h5ad", "--debug", "--port", "5005"])
         session = requests.Session()
         for i in range(90):
             try:

server/test/test_nan_rest.py

@@ -21,7 +21,7 @@ class WithNaNs(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         cls.ps = Popen(
-            ["cellxgene", "launch", "server/test/test_datasets/nan.h5ad", "--debug"]
+            ["cellxgene", "launch", "server/test/test_datasets/nan.h5ad", "--debug", "--port", "5005"]
         )
         session = requests.Session()
         for i in range(90):

server/utils/utils.py

@@ -0,0 +1,19 @@
+import contextlib
+import errno
+import socket
+
+
+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):
+        with contextlib.closing(socket.socket(socket.AF_INET, socket.SOCK_STREAM)) as s:
+            try:
+                s.bind((host, port_to_try))
+                return port_to_try
+            except socket.error:
+                pass
+    raise socket.error(errno.EADDRINUSE, f"No port in range {port} - {port + num_ports_to_try - 1} available.")