Opti-HPLC-Handler 3.7.0

SDK for interacting with the Waters Empower Web API.

OptiHPLCHandler

Software development kit (SDK) for interacting with the Waters Empower Web API. It aims to make putting data into and getting data out of Empower easy, with the aim of automating running samples. It will not feature changing data already in Empower.

Using the package

The package can be installed into a Python environment with the command

pip install Opti-HPLC-Handler

You can then import package and start an EmpowerHandler. You need to select the Empower project to log in to. Note that the user logging in needs to have access to both that project, and the project Mobile.

from OptiHPLCHandler import EmpowerHandler
handler=EmpowerHandler(
    project="project",
    address="https://API_url.com:3076",
    allow_login_without_context_manager=True,
)

Your username will be auto-detected. Add the argument username to circumvent this auto-detection.

EmpowerHandler will first try to find a password for Empower for the username in the OS's system keyring, e.g. Windows Credential Locker. If it can't access a system keyring, or the keyring does not contain the relevant key, you will be prompted you for the password. The password will only be used to get a token from the Empower Web API. When the token runs out, you will have to input your password again.

To log in, use the EmpowerHandler with a context manager:

handler=EmpowerHandler(
    project="project",
    address="https://API_url.com:3076",
)
with handler:
    ...

If you get the password from another source, e.g. a UI element, you can also manually log in with the password. In order to use this with a context manger, you need set EmpowerHandler to not log in when entering the context:

handler=EmpowerHandler(
    project="project",
    address="https://API_url.com:3076",
    auto_login=False,
)
with handler:
    handler.login(username="username", password="password")
    ...

When logged in, the EmpowerHandler can be used to access an authorisation key that can be used for the Web API directly:

handler.connection.authorization_header["Authorization"]

The authorisation key must be given in the HTTP header with the name Authorization. If you are using requests, you can simply provide handler.connection.authorization_header as headers in the request.

Instrument methods

You can now get a list of the instruement methods in the project:

method_list = handler.GetMethodList(method_type="Instrument")

You can get one such method and inspect its contents:

import pprint

pp = pprint.PrettyPrinter(indent=2)
full_method = handler.GetInstrumentMethod(method_name)
print(f"Valve positions: {full_method.instrument_method_list[-1].valve_position}")
print(f"Column temperature: {full_method.column_temperature}")
print("\n\nStart of gradient table:\n")
pp.pprint(full_method.gradient_table[0:2])

The created EmpowerInstrumentMethod object allows for changes, and remembers both the original method as it was in Empower, and the current mehtod with all changes made. It has the following properties:

• original_method
• current_method: The current method definition, with any changes applied.
• column_oven_list: A list of column ovens in the method set method. By default, only column managers are included, but you can include sample manager column ovens by creating it with handler.GetInstrumentMethod(method_name, use_sample_manager_oven=True).
• module_method_list
• solvent_handler_method: Will be None if no solvent handler is included in the method.
• column_temperature: If multiple column ovens are used, the temperature is only returned if all column ovens have the same temperature. Otherwise, a ValueError is raised. If no column ovens are found, a ValueError is raised. When setting the column temperature, all column ovens will be set to the same temperature, regardless of the original temperatures. If no column ovens are found, a ValueError is raised.
• gradient_table
• valve_position

Accessing or setting gradient_table or valve_position will result in a ValueError if no solvent handler is included in the method.

You can modify the method, give it a new name, and post it to Empower:

gradient_table = full_method.gradient_table
for step in gradient_table:
    step["Flow"] = 0.5
full_method.gradient_table = gradient_table
full_method.valve_position = ["A2", "B1"]
full_method.column_temperature = 40
full_method.method_name ="New method name"
with handler:
    handler.PostInstrumentMethod(full_method) # Post the updated method to Empower

Sampleset method

You can also get a list of the sample set methods in the project:

sampleset_list = handler.GetMethodList(method_type="SampleSet")

You can also get the plate types that can be used in the project, the method handler.GetPlateTypeNames is used. If you run it without arguments, it returns all possible plate type names. You can also give it a filter_string. In that case, only the plate types with names that contain the filter string are returned. You can then define the plate setup of your HPLC:

plate_type_name_list = handler.GetPlateTypeNames(filter_string="48")
plates = {"1": plate_type_name_list[0], "2": plate_type_name_list[1]}

You can also have the plate list be empty, but you will then have to fill it out in Empower before you can run the SampleSetMethod:

plates = {}

To create a new sampleset method, first create its sample list as a list of dictionaries. Each dictionary must have the keys SampleName. The key Method is intepreted as the Empower field MethodSetOrReportMethod, the key SamplePos as the Empower field Vial, and the key Injectionvolume as the Empower field InjVol. Note that if the dictionary contains both of one of these pairs, it is not predictable which will be used. Additional keys are interpreted as Empower fields with the key value as its name.

sample_list = [
    {
        "Method": method_list[0],
        "SamplePos": "1:A,1",
        "SampleName": "test_sample_name_1",
        "InjectionVolume": 1,
    },
    {
        "Method": method_list[1],
        "SamplePos": "2:A,1",
        "SampleName": "test_sample_name_2",
        "InjectionVolume": 2,
        "test_field_1": "test_value",
        "test_field_2" 2.3,
    },
]

At the moment, only Injection Sampleset lines are supported, but the injection volume can be set to 0.

At the moment, components can only be an empty list.

You can then use the handler to create the sampleset:

handler.PostExperiment(
    sample_set_method_name="test_sampleset_method_name",
    sample_list=sample_list,
    plates=plates,
    audit_trail_message="test_audit_trail_message",
)

To run the a SampleSetmethod, you need to provide a node name and a chromatograpic system name. If you don't know them, you can find them with handler.GetNodeName() and handler.GetSystemName(node = "node_name").

You can now run a sampleset method to create a sampleset:

handler.RunExperiment(
    sample_set_method="test_sampleset_method_name",
    sample_set_name="test_sample_set",
    node="node_name",
    system="test_hplc",
)

Getting started with developing the package

You can get the repo by cloning it from github at the URL https://github.com/novonordisk-research/OptiHPLCHandler.git.

If you can't clone the repo on a Windows machine, you might need to set the SSL backend. Run the following command in a terminal: git config --global http.sslbackend schannel

It is recommended to make and activate a virtual environment by running the following commands

pip install venv
python -m venv .env
.\.env\Scripts\activate

You need to run the last command every time you restart the computer.

When the virtual environment is activated, install the package locally as an editable installation:

pip install -e .[dev]

If this doesn't work, you might need to upgrade pip and/or setuptools:

.\.env\scripts\python.exe -m pip install --upgrade pip
.\.env\scripts\python.exe -m pip install --upgrade setuptools

You should then be able to install the package locally as an editable installation.

Releasing

To release a new version, get all of the changes you want into the branch main. Then manually run the release GitHub action by clicking Run workflow. Select what type of release it is (patch, minor, or major) in The type of release to perform, and then click Run workflow.

The workflow should create a branch, a tag, a pull request, a Github release and a pypi release.

After the workflow is done, you need to approve the pull request.