structure rebuild: bugfix. Works with PSI_test package

DataManager/executioner.py

@@ -12,7 +12,7 @@ def __init__(self, q, q_new_item, device_details, thread_name, experimental_deta
         """
         :param q: queue.Queue() object, commands are put in it
         :param q_new_item: queue.Event() object, is set when new commands are added to it, which triggers the checker
-        :param device_details:  dict, check documentation.txt
+        :param device_details:  dict, check wiki
         :param thread_name: name of the thread, used to identify and keep in tact active threads
         """
         thread_name = thread_name+'-checker'

commandInterpreter/base_interpreter.py

@@ -78,7 +78,8 @@ def device_con(self, id, args):
                 return result
             except TypeError:
                 raise Exception('Invalid input')
-            except Exception:
+            except Exception as e:
+                print(e)
                 count += 1
                 sleep(0.1)
 

commandInterpreter/interpreterPBR.py

@@ -19,7 +19,7 @@ def initial_od(self):
         while len(data) < 5:
             try:
                 data.append(self.device_con(5, '[1]'))
-            except Exception:
+            except Exception as e:
                 # in case of connection error, log it
                 time_issued = datetime.datetime.utcnow()
                 time_issued = time_issued.strftime("%Y-%m-%d %H:%M:%S")
@@ -54,19 +54,23 @@ def __init__(self, device_details, q, q_new_item, log, device_class, experiment_
         self.q = q
         self.q_new_item = q_new_item
         self.pump_state = [False]
+        self.log = log
+        self.device_details = device_details
+        self.device_class = device_class
 
-        self.OD_checker = OD_Checker.ODcheck(self.device_details,
+        self.OD_checker = OD_Checker.ODcheck(device_details,
                                              self.q,
                                              self.q_new_item,
-                                             self.initial_od(),
+                                             0,
                                              self.pump_state)
 
-        super(DeviceManager, self).__init__(device_details,
-                                            device_class,
-                                            log,
+        super(DeviceManager, self).__init__(self.device_details,
+                                            self.device_class,
+                                            self.log,
                                             self.pump_state,
                                             self.OD_checker,
                                             experiment_details)
+
         self.commands = {
             1: self.device.get_temp_settings,
             2: self.device.get_temp,
@@ -92,6 +96,7 @@ def __init__(self, device_details, q, q_new_item, log, device_class, experiment_
             22: self.device.get_hardware_address,
             23: self.device.get_cluster_name
         }
+
         try:
             self.device_con(8, str([device_details['setup']['pump_id'], False]))
         except Exception:
@@ -107,3 +112,10 @@ def __init__(self, device_details, q, q_new_item, log, device_class, experiment_
         }
         )
 
+        initial_od = self.initial_od()
+        self.OD_checker.average = initial_od
+
+        if self.device_class == "Phenometrics":
+            self.device.pump_manager.last_OD = initial_od
+            self.device.pump_manager.stored_OD = initial_od
+

server/DBapp.py

@@ -296,8 +296,8 @@ class ApiInit:
 
     def __init__(self):
         self.app = Flask(__name__)
-        script_location = Path(__file__).absolute().parent
-        with open(str(script_location / 'server_config.json'), 'r') as config_file:
+        self.script_location = Path(__file__).absolute().parent
+        with open(str(self.script_location / 'server_config.json'), 'r') as config_file:
             config = load(config_file)
             # if no auth is specified in config, no auth will be required
             self.app.config['USERNAME'] = config.get('username', None)
@@ -320,7 +320,9 @@ def run_app(self):
         :return: None, process is stuck on app.run() 
         """
         context = ssl.SSLContext(ssl.PROTOCOL_TLSv1_2)
-        context.load_cert_chain('MyCertificate.crt', 'MyKey.key')
+        context.load_cert_chain(str(self.script_location / 'MyCertificate.crt'),
+                                str(self.script_location / 'MyKey.key'))
+
         self.app.run(host='0.0.0.0', ssl_context=context)
 
     def run(self):

server/protocolChecker.py

@@ -32,29 +32,29 @@ def check_protocol(self, protocol):
         for node in protocol:
             for node_key in self.node_keys:
                 if node_key not in protocol[node]:
-                    missing.append("Node %s is missing %s" % (node, node_key))
+                    missing.append("Node %s is missing %s. " % (node, node_key))
 
             for experiment_key in self.experiment_keys:
                 if experiment_key not in protocol[node].get('experiment_details', {}):
-                    missing.append("Node %s is missing %s in experiment_details" % (node, experiment_key))
+                    missing.append("Node %s is missing %s in experiment_details. " % (node, experiment_key))
 
             device_counter = 0
             for device in protocol[node].get('devices', {}):
 
                 for device_key in self.device_keys:
                     if device_key not in device:
                         missing.append(
-                            "VirtualDevice %d on Node %s is missing %s" % (device_counter, node, device_key))
+                            "VirtualDevice %d on Node %s is missing %s. " % (device_counter, node, device_key))
 
                 if 'device_type' in device and device['device_type'] == 'PBR':
                     for setup_key in self.PBR_setup:
                         if setup_key not in device.get('setup', {}):
                             missing.append(
-                                "PBR on Node %s is missing %s in its setup" % (node, setup_key))
+                                "PBR on Node %s is missing %s in its setup. " % (node, setup_key))
                 if 'device_class' in device:
                     for key in self.device_variants[device['device_class']]:
                         if key not in device:
-                            missing.append("VirtualDevice of %s is missing %s" % (device['device_class'], key))
+                            missing.append("VirtualDevice of %s is missing %s. " % (device['device_class'], key))
                 device_counter += 1
 
         return missing