From 81546a1c8db82cdcb80c13917bc0fc5ac0c50e25 Mon Sep 17 00:00:00 2001
From: Joel Collins <joel@jtcollins.net>
Date: Tue, 26 May 2020 13:18:09 +0100
Subject: [PATCH 1/2] Add timeout support

---
 .../stage/sangaboard/extensible_serial_instrument.py       | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/openflexure_microscope/stage/sangaboard/extensible_serial_instrument.py b/openflexure_microscope/stage/sangaboard/extensible_serial_instrument.py
index 6e993d3e..ce98acbe 100644
--- a/openflexure_microscope/stage/sangaboard/extensible_serial_instrument.py
+++ b/openflexure_microscope/stage/sangaboard/extensible_serial_instrument.py
@@ -78,6 +78,7 @@ class ExtensibleSerialInstrument(object):
         then we don't warn when ports are opened multiple times.
         """
         with self.communications_lock:
+            logging.debug(f"Opening port {port}")
             if hasattr(self, "_ser") and self._ser.isOpen():
                 if not quiet:
                     logging.warning("Attempted to open an already-open port!")
@@ -133,9 +134,12 @@ class ExtensibleSerialInstrument(object):
             assert (
                 self._ser.isOpen()
             ), "Attempted to write to the serial port before it was opened.  Perhaps you need to call the 'open' method first?"
+            logging.debug("Encoding message...")
             data = query_string + self.termination_character
             data = data.encode()
+            logging.debug(f"Writing message: {data}")
             self._ser.write(data)
+            logging.debug("Write successful")
 
     def flush_input_buffer(self):
         """Make sure there's nothing waiting to be read, and clear the buffer if there is."""
@@ -145,6 +149,7 @@ class ExtensibleSerialInstrument(object):
 
     def readline(self, timeout=None):
         """Read one line from the serial port."""
+        self._ser.timeout = timeout
         with self.communications_lock:
             return (
                 self._ser.readline()
@@ -192,7 +197,9 @@ class ExtensibleSerialInstrument(object):
         """
         with self.communications_lock:
             self.flush_input_buffer()
+            logging.debug(f"Writing query: {queryString}")
             self.write(queryString)
+            logging.debug("Waiting for query response...")
             if self.ignore_echo == True:  # Needs Implementing for a multiline read!
                 first_line = self.readline(timeout).strip()
                 if first_line == queryString:

From a0702fbc6977e586bfbc182cb49ba2850fc2fe28 Mon Sep 17 00:00:00 2001
From: Joel Collins <joel@jtcollins.net>
Date: Tue, 26 May 2020 13:22:14 +0100
Subject: [PATCH 2/2] Set logging level further up the script

---
 openflexure_microscope/api/app.py | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/openflexure_microscope/api/app.py b/openflexure_microscope/api/app.py
index 0f08b7f7..329c68aa 100644
--- a/openflexure_microscope/api/app.py
+++ b/openflexure_microscope/api/app.py
@@ -6,6 +6,11 @@ monkey.patch_all()
 import time
 import atexit
 import logging, logging.handlers
+
+# Set root logger level
+logger = logging.getLogger()
+logger.setLevel(logging.DEBUG)
+
 import os
 import pkg_resources
 
@@ -42,16 +47,12 @@ formatter = logging.Formatter(
 )
 
 
-# Get root logger
-logger = logging.getLogger()
-logger.setLevel(logging.INFO)
-
 # Create file handler
 fh = logging.handlers.RotatingFileHandler(
     ROOT_LOGFILE, maxBytes=1_000_000, backupCount=5
 )
 fh.setFormatter(formatter)
-fh.setLevel(logging.INFO)
+fh.setLevel(logging.DEBUG)
 fh.propagate = False
 
 # Create access log file handler
@@ -59,7 +60,7 @@ afh = logging.handlers.RotatingFileHandler(
     ACCESS_LOGFILE, maxBytes=1_000_000, backupCount=5
 )
 afh.setFormatter(formatter)
-afh.setLevel(logging.INFO)
+afh.setLevel(logging.DEBUG)
 afh.propagate = False
 
 # Add file handler to root logger
@@ -157,10 +158,12 @@ def err_log():
         attachment_filename="openflexure_microscope_{}.log".format(timestamp),
     )
 
-@app.route('/api/v1/', defaults={'path': ''})
-@app.route('/api/v1/<path:path>')
+
+@app.route("/api/v1/", defaults={"path": ""})
+@app.route("/api/v1/<path:path>")
 def api_v1_catch_all(path):
-    abort(410, 'API v1 is no longer in use. Please upgrade your client.')
+    abort(410, "API v1 is no longer in use. Please upgrade your client.")
+
 
 # Automatically clean up microscope at exit
 def cleanup():