Smart Spectal Matching Python Client Library

Smart Spectral Matching Python Client

Installation

Using pip

coming soon...

Manually

Clone the repository either via:

• HTTP:

git clone https://github.com/smart-spectral-matching/ssm-client-python.git

• SSH:

git clone git@github.com:smart-spectral-matching/ssm-client-python.git

Create a virtual environment and activate to install the package in the isolated environment:

python -m venv <name of env>
source <env>/bin/activate

To install the package from the local source tree into the environment, run:

python -m pip install .

Or to do so in "Development Mode", you can run:

python -m pip install -e .

To deactivate the virtual environment

deactivate

When finished, remove the virtual environment by deleting the directory:

rm -rf <name of env>

Usage

After installation, you can use the two main components of this package for the following functions:

• ssm_client.io - Spectroscopy file format translations
• ssm_client.SSMRester - REST API client for data management

Also, there are Jupyter Notebooks in the tutorials/ directory to help get started and test files under tests/data in different directories.

IO Module

This module is used to translate to and from different spectroscopy file formats. The currently supported file formats are:

• JCAMP-DX
• RRUFF

The module has two main functions, read and write.

The read function reads in spectroscopy files and translates them to SciData JSON-LD dictionaries.

The write function takes SciData JSON-LD dictionaries and writes them out in the specified spectroscopy file format.

Example:

from ssm_client.io import read, write

# Read in from RRUFF, write out to JCAMP-DX
scidata_dict = read("./tests/data/rruff/raman_studtite.rruff", ioformat="rruff")
write("./raman_studtite.jdx", scidata_dict, ioformat="jcamp")

# Modify SciData JSON-LD and write back out to RRUFF
uid = 'my:example:jsonld'
scidata_dict["@graph"]["uid"] = uid
write("./my_raman_studtite.rruff", scidata_dict, ioformat="rruff")

SSMRester

The SSMRester is a REST client for the SSM REST API for storing datasets.

The SSMRester is a class and you can create an object by providing the REST API server information (hostname + port) you want to interact with for uploading / downloading datasets.

A dataset is a collection of individual data you want to store and a model is the individual data you store as a graph.

You must have a dataset that a model is associated with.

With a SSMRester object, you can perform common Create-Read-Update-Delete (CRUD) tasks for datasets and models.

Example:

import json
from ssm_client import SSMRester

rester = SSMRester(hostname="http://ssm.ornl.gov")
dataset = rester.dataset.create()
rester.initialize_model_for_dataset(dataset)

model = rester.model.create(scidata_dict)
print(dataset.uuid)
print(model.uuid)
rester.dataset.delete_by_uuid(dataset.uuid)

Development

Install via pdm

Install via pdm with dev dependencies:

pdm install -G:all

Then, run commands via pdm:

pdm run python -c "import ssm_client"

Tests / Linting

Flake8 linting

Run linting over the package with flake8 via:

pdm run flake8 src/ssm_client/ tests/

Pytest testing

Run tests using pytest:

pdm run pytest tests/

Code coverage

Get code coverage reporting using the pytest-cov plugin:

pdm run pytest --cov=src/ssm_client --cov-report=term-missing tests/

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update tests as appropriate.

Links

• SSM Python Client Project GitHub Repository: https://github.com/smart-spectral-matching/ssm-client-python
• SSM File Converter Service GitHub Repository: https://github.com/smart-spectral-matching/ssm-service-file-converter
• SSM Catalog Service GitHub Repository: https://github.com/smart-spectral-matching/ssm-service-catalog

Licensing

BSD 3-clause