Add example python scripts

Signed-off-by: Lukas Bromig <lukas.bromig@tum.de>

docs/source/04_How-To.rst

@@ -45,7 +45,7 @@ investigate which (observable) commands and (observable) properties are implemen
 commands and properties shows the user useful information on functionality and usage. Required parameters and responses
 are displayed with the attributed SiLA-datatype.
 
-.. image:: _static/figures/devices.png
+.. image:: /docs/source/_static/figures/devices.png
     :width: 800
     :alt: A view of the main page, the devices list, including general device details
 
@@ -59,13 +59,13 @@ basic information it was registered with by the server. This information is used
 dynamic client. The client files are stored in the local temporary folder named after the devices server-UUID:
 Relative path to the directory: *[...]temp/device-manager/SiLA/<device-UUID>/*
 
-.. image:: _static/figures/discovery.png
+.. image:: docs/source/_static/figures/discovery.png
     :width: 800
     :alt: A view of the discovery feature for adding new devices to the manager
 
 SiLA Explorer - The device tree
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Each device is that is added to the device manager is assigned an internal UUID. This way devices with the same server
+Each device that is added to the device manager is assigned an internal UUID. This way devices with the same server
 name can be uniquely identified. The device tree enables the user to run commands and request properties interactively
 from within the browser. On the lowest level of the device tree, the command/property level, a run button can be clicked
 to execute the function. For functions that require user input, the parameters can be entered in the corresponding text

examples/database_example.py

@@ -0,0 +1,36 @@
+from influxdb import InfluxDBClient
+from datetime import datetime
+import numpy as np
+import time
+
+# Instantiate the database client.
+influx_client = InfluxDBClient(host='localhost', port=8086, username='root', password='root', database='device_manager')
+
+# Check connection
+print(f'Checking connectivity. DB server version: {influx_client.ping()}')
+
+for i in range(0, 100, 1):
+    # This is an example write operation
+    data_point = {
+        "measurement": "testMeasurement",
+        "tags": {
+            "experiment_name": "influxDB_test"
+        },
+        "time": datetime.now().strftime("%Y-%m-%dT%H:%M:%SZ"),
+        "fields": {
+            "test_number": np.random.rand(1)
+        }
+    }
+
+    try:
+        influx_client.write_points([data_point])
+    except:
+        print("This did not work...")
+
+    # This is an example query.
+    results = influx_client.query(
+        'SELECT test_number FROM "device_manager"."autogen"."testMeasurement" WHERE experiment_name = \'influxDB_test\' GROUP BY position'
+        'ORDER BY DESC LIMIT 1')
+    print(results)
+
+    time.sleep(10)

examples/device_example.py

@@ -0,0 +1,16 @@
+import devices
+
+# WIP
+# This example will show you how to import a device client
+# This is work in progress
+
+# ...
+yourObject = devices['HelloSiLA_server']()
+# You can call functions as described for every command and property in the device feature explorer under "Usage"
+# To call the property "StartYear" of the HelloSiLA example device use:
+StartYear = yourObject.call_property("GreetingProvider","StartYear")
+
+# To run the "SayHello" command use:
+response = yourObject.call_command("GreetingProvider","SayHello",parameters={"Name": 'some name'})
+
+# Note: you need to replace the "yourObject" part of the command with the client object of that device!

examples/fermentation_example.py

@@ -0,0 +1,122 @@
+import time
+import numpy as np
+import devices
+import interface.DASGIP.DASGIP_Service.DASGIP_Service_client as client
+import logging
+import pandas
+
+
+def initialize_logging():
+    # initialize logging
+    logger = logging.getLogger(__name__)
+    logger.setLevel(logging.DEBUG)
+    logger.propagate = False
+
+    formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
+
+    # file handler
+    filehandler = logging.FileHandler(__file__ + '.log', mode='a')
+    filehandler.setLevel(logging.INFO)
+    filehandler.setFormatter(formatter)
+    logger.addHandler(filehandler)
+
+    # console handler, i.e. output to command window
+    console_handler = logging.StreamHandler()
+    console_handler.setLevel(logging.DEBUG)
+    console_handler.setFormatter(formatter)
+    logger.addHandler(console_handler)
+
+    return logger
+
+
+def start_feed_pump(reactor_client, units: list):
+    """ Start reactor feed pump C of the reactor """
+    for unit in units:
+        reactor_client.PumpCServicer_SetCmd(unit, 2)
+
+
+def stop_feed_pump(reactor_client, units):
+    """ Stop reactor feed pump C of the reactor """
+    for unit in units:
+        reactor_client.PumpCServicer_SetCmd(unit, 1)
+
+
+def calculate_pump_duration(elapsed_time: float, feed_rate: float, pump_rate: float):
+    """ Calculates the time the pump must run to transfer a discrete volume  """
+    volume_to_pump = (elapsed_time / 60) * feed_rate  # feed rate has the unit ml/h, elapsed time has the unit minutes
+    logger.info(f'The volume to pump is {volume_to_pump}')
+    pump_time_min = (volume_to_pump / pump_rate) * 60  # pump rate has the unit ml/h
+    return pump_time_min
+
+
+if __name__ == '__main__':
+    # Instantiate the devices
+    reactor_client = devices['DasgipService']()
+    offgas_analytics_client = devices['BlueVaryService']()
+    external_pump_client = devices['RegloICCService']()
+
+    # Instantiate database client
+
+    # Instantiate logging
+    logger = initialize_logging()
+
+    # Define process parameter variables
+    reactor_units = [0, 2]   # 0-based counting
+    reactor_pump_rate = 40   # The applied pump rate in the reactor, in this case max rate is used
+    reactor_feed_rate = 2.4  # Total feed rate in ml / h
+    experiment_duration = 16 * 60 * 60
+    increment = 0.1
+
+
+    # Import the discrete substrate addition times and volumes from an external file
+    df_feeding_intervals = pandas.read_csv("feeding_interval.csv")
+    print(df_feeding_intervals)
+    feed_intervals = df_feeding_intervals['time_interval, min']
+    print(feed_intervals)
+
+    # Set initial pump rate, avoids manual work
+    for reactor_unit in reactor_units:
+        # Set reactor feed pump setpoints
+        reactor_client.PumpCServicer_SetSetpointSelect(reactor_unit, 1)
+        reactor_client.PumpCServicer_SetSPM(reactor_unit, reactor_pump_rate)
+    logger.info(f'Setpoint is set to {reactor_pump_rate} ml/h for the units {reactor_units}')
+
+    # Start of the main loop
+    experiment_start_time = time.time()
+    start_time = time.time()
+    logger.info(f' Start time is {start_time}')
+    # Iterate over the discrete entries of feeding events in the file to simulate an intermittent feeding strategy
+    # with a peristaltic pump in a L-scale fermenter
+    for index, off_timer in feed_intervals.items():
+        exit_criterion: bool = False
+        delta_t: float = 0
+
+        # Wait for the off-timer to elapse
+        logger.debug(f'Waiting for off-timer ({off_timer}) to elapse')
+        # We wait until the next feeding event is reached
+
+        while delta_t < off_timer:
+            if time.time() >= (experiment_start_time + experiment_duration):
+                # If the defined experiment duration is reached, the exit procedure is initiated
+                logger.debug(f'Exiting experiment main loop at {time.time()}/ {experiment_start_time + experiment_duration}')
+                exit_criterion = True
+                break
+            time.sleep(increment)
+            delta_t = (time.time() - start_time) / 60
+
+        if exit_criterion:
+            # break out of the for-loop
+            break
+        # Re-initialize the start time while the pump is working
+        start_time = time.time()
+        logger.info(f' Start time is {start_time}')
+
+        # Pump the desired volume while the off-timer starts to elapse
+        pump_time_min = calculate_pump_duration(elapsed_time=off_timer, feed_rate=reactor_feed_rate, pump_rate=reactor_pump_rate)
+        logger.info(f'The scheduled pump run time in minutes is {pump_time_min}')
+
+        # Start the pump
+        start_feed_pump(reactor_client=reactor_client, units=reactor_units)
+        time.sleep(pump_time_min)
+        # Stop the pump
+        stop_feed_pump(reactor_client=reactor_client, units=reactor_units)

examples/hello_world.py

@@ -0,0 +1,5 @@
+# You can use this code editor like a regular scripting environment.
+# If you require specific python packages for your script, you can import them here.
+# Note: Packages you want to import must be specified in the dockerfiles requirements.txt!
+
+print("Hello World!")

setup_test_db.py

@@ -448,7 +448,7 @@
                 '# To call the property "StartYear" of the HelloSiLA example device use:\n'
                 'StartYear = yourObject.call_property("GreetingProvider","StartYear")\n\n'
                 '# To run the "SayHello" command use:\n'
-                'response = yourObject.call_command("GreetingProvider","SayHello",parameters: { "Name": })\n\n'
+                'response = yourObject.call_command("GreetingProvider","SayHello",parameters={"Name": \'some name\'})\n\n'
                 '# Note: you need to replace the "yourObject" part of the command with the client object of that device!'
     },
     {
@@ -458,12 +458,13 @@
         'data': 'from influxdb import InfluxDBClient\n'
                 'from datetime import datetime\n'
                 'import numpy as np\n\n\n'
+                'import time'
                 '# Instantiate the database client.\n'
                 'influx_client = InfluxDBClient(host=\'localhost\', port=8086, username=\'root\', password=\'root\', database=\'device_manager\')\n\n'
                 '# Check connection\n'
                 'print(f\'Checking connectivity. DB server version: {influx_client.ping()}\')\n\n'
                 'for i in range(0, 100, 1):\n'
-                '# This is an example write operation\n'
+                '\t# This is an example write operation\n'
                 '\tdata_point = {\n'
                 '\t\t"measurement": "testMeasurement",\n'
                 '\t\t"tags": {\n'