elsci-peaksel-sdk 1.3.0

SDK to upload and manage chromatographic injections and other data in Elsci Peaksel

Peaksel SDK (Python)

A library to manage chromatography data in Peaksel: upload raw data, fetch the results of parsing (spectra, traces, peaks, injection info, etc).

If you need some advanced processing (like peak deconvolution), you can combine it with:

• MOCCA for DAD/PDA spectral processing for peak deconvolution, purity and yield calculations
• matchms for Mass Spec (especially Tandem MS) spectral processing, as well as isotopic pattern score matching and searching, and other machine learning capabilities.

To install Peaksel SDK:

pip install elsci-peaksel-sdk

Examples

Read public data

First, we're going to read an already uploaded injection (like this one), and print some spectra info from each detector:

from peakselsdk.Peaksel import Peaksel

# Initialize the entry point:
peaksel = Peaksel("https://peaksel.elsci.io", org_name="elsci")

# Fetch injection info:
injection = peaksel.injections().get("8ehCv4tVR1U")

# Go through all detectors and print the spectra:
for detectorRun in injection.detectorRuns:
    if not detectorRun.has_spectra():
        continue
    spectra = peaksel.blobs().get_spectra(detectorRun.blobs.spectra)  # fetch spectra
    for spectrum in spectra:
        print(f"{spectrum.rt}: {spectrum.x}")

Uploading & parsing vendor files

If you want to upload an injection or read private data, you must authenticate. The general steps stay similar though:

from peakselsdk.Peaksel import Peaksel

org = "YOUR ORG NAME"  # or your username if you want to work with your personal data
auth_header = {"Cookie": "SESSION=YOUR SESSION ID"}  # either cookie or Basic Auth
raw_data = "/path/to/zip/with/raw-data.zip"

# Entry point to Peaksel:
peaksel = Peaksel("https://peaksel.elsci.io", org_name=org, default_headers=auth_header)

# Upload & parse, get the ID back:
injection_ids = peaksel.injections().upload(raw_data) 

# Fetch injection info:
injection = peaksel.injections().get(injection_ids[0])

# Now you can do the same operations as in the previous example
# ...

Before running this:

1. You need to register at Peaksel Hub, get a private SaaS or install Peaksel on your machines.
2. Determine how you want to authenticate (service account or SessionID, see the next section)

Authentication

Session ID auth (Cookie)

If you're just playing, you can run the code on behalf of your own account:

auth_header = {"Cookie": "SESSION=YOUR SESSION ID"}

You can get this cookie from the browser:

1. In Chrome: open Peaksel -> authenticate -> Press F12
2. Go to Application tab -> Cookies -> click on the website URL -> copy the Value of the JSESSIONID cookie

Service Accounts auth (Basic Auth)

Service accounts can have their Basic Auth credentials specified in Peaksel configs. This option is available in Private SaaS and on-prem installations. For Peaksel Hub you need to request it ([e-mail]). If you go with Basic Auth, then in the code you set up auth headers this way:

from peakselsdk.util.api_util import peaksel_basic_auth_header

auth_header = {"Authorization": peaksel_basic_auth_header("your username", "your password")}

Design & Conventions

All the necessary functionality is exposed from peakselsdk.Peaksel class - just use its methods to work with Injections, Batches, Substances (analytes), Peaks, etc.

• XxxClient are classes to communicate with the app API, they are created and returned by Peaksel entrypoint
• Classes like User, Org, Injection capture the actual requests and responses
  • Fields are camelCased to match the JSON structure
  • The JSON's id is actually stored in eid (aka entity id) in the classes. Because id has special meaning in Python.
  • Every __init__() has **kwargs param that is ignored. This is needed to simplify parsing of response JSONs, as we always keep the names in the classes and JSONs the same, so when passing those as dict into the constructor, the corresponding fields are set. But it's possible that in Peaksel we add a new param, and this would break dict->DTO conversion as the param will be unknown. So to be forward-compatible, we add **kwargs to capture all the unknown fields.

Working with source code

1. Install uv build tool and run: uv venv && uv sync && uv build
2. In PyCharm mark src as Sources Root and test as Test Sources Root
3. To run the tests ./test.sh