Smart Spectral Matching Python Client
coming soon...
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>
After installation, you can use the two main components of this package for the following functions:
ssm_client.io- Spectroscopy file format translationsssm_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.
This module is used to translate to and from different spectroscopy file formats. The currently supported file formats are:
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")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)Install via pdm with dev dependencies:
pdm install -G:all
Then, run commands via pdm:
pdm run python -c "import ssm_client"
Run linting over the package with flake8 via:
pdm run flake8 src/ssm_client/ tests/
Run tests using pytest:
pdm run pytest tests/
Get code coverage reporting using the pytest-cov plugin:
pdm run pytest --cov=src/ssm_client --cov-report=term-missing tests/
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.
- 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