Package: covmatic-stations
StationsThis software is part of theCovmaticproject.Visit the websitehttps://covmatic.org/for more documentation and information.:warning:This package is meant to be directly used only by an informed developer audienceNon-devs can more easily access the protocols implemented in this package via the Covmatic LocalWebServer GUITable of ContentsInstallationRobot network configurationUsageLoggingCopan 48 rackMagnet settingsTestingInstallationYou caninstall the Covmatic Stations package viapip:<python> -m pip install covmatic-stationsWhere<python>should be changed for the Python instance you wish to install the LocalWebServer onto. We will be following this convention for all the next instructions.Robot network configurationSee theconfigfolder for robot network configuration protocols.UsageIn theprotocolsdirectory you can find usage examples.First, you have to import the station you want to use.
In this example (protocols/station_a_technogenetics.py),
we will use the Station A class for the Technogenetics kit that uses custom 4x6 COPAN tube racks.from covmatic_stations.a.technogenetics import StationATechnogenetics24Then, you have to instantiate your own station.
All classes come with a full set of default parameters,
that you can change to suit your needs.
E.g. let's assume you want to change the number of samples to 96.station = StationATechnogenetics24(num_samples=96)You can also specify your language:'ENG'(default) or'ITA'.
This choice will affect the messages that the internal protocol server sends to the LocalWebServer.
E.g.station = StationATechnogenetics24(
    num_samples=96,
    language="ITA"
)You also have to define the metadata (at least the API level) as usualmetadata = {'apiLevel': '2.3'}Finally, the definition of therunfunction becomes trivialdef run(ctx):
    return station.run(ctx)Extend stationsIf you want to customize your station further than what changing parameters allows, you can create your own station class.
First identify the base stations that you want to customize (e.g.StationBTechnogenetics).You want to create a new class that extends that base class.
The methodbodyimplements the core of the protocol instructions.
Labware and instrument initialization is done before the body. Cleanup is done after.To change the protocol procedure, overridebody.If you want not to load a labware piece (or instrument), identify the corresponding loader method:
it should be tagged by a@labware_loader(or@instrument_loader) decorator.:warning: The method may be implemented by a parent class of the class you are looking at.
If you don't find the method in the class you are extending, look in the parent classes.If you want to load a new labware piece (or instrument), define a corresponding loader method:
it should be decorated by a@labware_loader(or@instrument_loader) decorator.
The decorators take two argumentsindex: labware and instruments are loaded in the order defined by these indices (first all the labware, then all the instruments)name: the name of the labware or instrument (for debug purposes)An example of protocol file made by extending a station class could beimport logging
from covmatic_stations.b.technogenetics import StationBTechnogenetics


class CustomStation(StationBTechnogenetics)
    # override loader: tempdeck will not be loaded
    def load_tempdeck(self):
        pass
    
    # load a custom labware piece
    @labware_loader(10, "_custom_labware")
        self._custom_labware = self._ctx.load_labware(...)
    
    # override body: redefine the procedure
    def body(self)
        ...

# debug level brings up more log messages, try this when extending a new class
logging.getLogger(CustomStation.__name__).setLevel(logging.DEBUG)
metadata = {'apiLevel': '2.3'}
station = CustomStation(num_samples=96)


def run(ctx):
    return station.run(ctx):warning: If you are using the LocalWebServer GUI to upload the protocol file
store this custom file in a different path than the one used for the automatically generated protocolTo upload this custom file using the LocalWebServer GUI:Savethe automatically generated protocol to a fileCopythe custom file to overwrite the automatically generated protocolUploadthe file (press the upload button)Verifythat the uploaded file is the correct oneRead the confirmation message: you should read that the expecte file has been uploadedIf the robot's Jupyter server is on, you can directly overwrite the protocol file on the robot via the Jupyter interface.LoggingYou can adjust the logging level of your station (e.g. toINFO) like soimport logging
logging.getLogger(StationAP300.__name__).setLevel(logging.INFO)By default, the level is set toDEBUG.Copan 48 Rack correctionThe station A protocols use a custom tube rack.
The rack definition is generated by the corresponding class.
Some fine redefinition may be needed.
You can adjust the definition with a JSON file.
All values in the JSON file are considered multipliers. E.g.{
  "stagger": 1.27,
  "distance_vert": 0.98
}This file specifies astaggervalue 27% bigger than the theoretical value
and adistance_vertvalue 2% smaller than the theoretical value.If the default value is a tuple, use a list of multipliers. E.g.{
  "global_dimensions": [1, 1.2, 0.9]
}To override the default adjustments,
you can set the environment variableOT_COPAN_48_CORRECTto the file path of your
custom JSON.Magnet SettingsMagnet settings are read from a JSON file in the package.
To override the file path, you can set the environment variableOT_MAGNET_JSONto your custom path (a path on the OT's Raspberry).
If the file was/home/altern_magnet.json, you would have to writeexport OT_MAGNET_JSON=/home/altern_magnet.jsonTo delete the variable you can rununset OT_MAGNET_JSONThe JSON file should be an array of objects, each of which has the fieldsserial,stationandheight. E.g.[
  {
	"serial": "X",
	"station": "B1",
	"height": 6.20
  },
  {
	"serial": "Y",
	"station": "B2",
	"height": 6.20
  }
]To inspect a field of a magnet, use the following patternmagnets.<field>.by_<key>["keyvalue"]. E.g. to get the height of the magnet whose serial isXyou would writefrom covmatic_stations.b import magnets
h = magnets.height.by_serial["X"]TestingThe package comes with some unit tests. If you want to run them then checkout the code, move to the code folder, install the package with:py setup.py installand then run the tests with:pytest