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https://github.com/synbiodex/excel-to-sbol
https://github.com/synbiodex/excel-to-sbol
Last synced: 4 days ago
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- Host: GitHub
- URL: https://github.com/synbiodex/excel-to-sbol
- Owner: SynBioDex
- License: bsd-3-clause
- Created: 2020-09-16T15:33:58.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2022-11-02T18:20:10.000Z (about 2 years ago)
- Last Synced: 2024-04-26T13:40:16.387Z (9 months ago)
- Language: Python
- Size: 68.3 MB
- Stars: 4
- Watchers: 4
- Forks: 7
- Open Issues: 19
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Excel-to-SBOL
**Excel-to-SBOL** is an open source python library that converts [Excel Templates](https://github.com/SynBioDex/Excel-to-SBOL/tree/master/excel2sbol/resources/templates) to [SBOL](https://sbolstandard.org/) documents.
A similar utility developed for SBOL3 support (developed by Jake Beal) is [SBOL-utilities](https://github.com/SynBioDex/SBOL-utilities).
For further depth and information on Excel-to-SBOL, including how to contribute to the project, visit the [Excel-to-SBOL wiki on github](https://github.com/SynBioDex/Excel-to-SBOL/wiki)
# Table of Contents
- [Installation & How to Use](#installation--how-to-use)
- [Installation](#installation)
- [How to Use](#how-to-use)
- [Example Conversion](#example-conversion)
- [Architecture](#architecture)
- [Publishing](#publishing)
# Excel-to-SBOL: Installation & How to use
## Installation
Excel-to-SBOL can be installed using `pip install excel2sbol`
To get the latest version you can use `git clone https://github.com/SynBioDex/Excel-to-SBOL` followed by `cd .\excel2sbol` and `python setup.py install`
## How to use
**1) Choose an Excel Template**
Choose an excel template from the [templates folder](https://github.com/SynBioDex/Excel-to-SBOL/tree/master/excel2sbol/resources/templates).
We suggest choosing the latest version (dates are given at the end of the file names in the form yyyymmdd). Fill out the template as the instructions indicate.
**2) Install the Converter**
There are several ways to install the converter. The easiest is via pip: `pip install excel2sbol` but it can also be done by [cloning the repository](https://github.com/SynBioDex/Excel-to-SBOL/wiki/2.-Cloning-From-GitHub).
**3) Run the Converter**
Use the code below substituting {things in curly brackets} with the appropriate values.
```
import excel2sbol.converter_function as conf
conf.converter({template_name}, {file_path_in}, {file_path_out})
```
An example:
```
import excel2sbol.converter_function as conf
conf.converter("excel2bol_darpa_template_blank_v005_20220222.xlsx",
"C:/Users/Test_User/Downloads/Filled_Template.xlsx",
"C:/Users/Test_User/Downloads/Output_SBOL.xml")
```
Tip: the use of `os.getcwd()` and `os.path.join` is reccommended for the creation of the file paths. This is safer from a cybersecurity stand point and provide better operating system interoperability.
**4) Use the output file**
The SBOL file that is output can then be used by further [SBOL tools](https://sbolstandard.org/applications/) or uploaded to an SBOL repository like [SynBioHub](https://synbiohub.org/).
# Example Conversion
A data-filled [spreadsheet](https://github.com/SynBioDex/Excel-to-SBOL/blob/master/excel2sbol/tests/test_files/pichia_toolkit_KWK_v002.xlsx) was converted to an [SBOL file](https://github.com/SynBioDex/Excel-to-SBOL/blob/master/excel2sbol/tests/test_files/pichia_toolkit_KWK_v002.xml) and subsequently [uploaded to SynBioHub](https://synbioks.org/public/pichia_toolkit_KWK/pichia_toolkit_KWK_collection/1).
**Example Spreadsheet**
**Example SBOL**
**Example SynBioHub Upload**
# Architecture
The [repository architecture and module architecture](https://github.com/SynBioDex/Excel-to-SBOL/wiki/4.-Excel2SBOL-Module-and-Repository-Architecture) are described in the wiki.
# Publishing
A new version of the python package is automatically published via [the python-publish GitHub action](https://github.com/SynBioDex/Excel-to-SBOL/blob/master/.github/workflows/python-publish.yml) whenever a new release is created.
Alternatively you can also make changes to the package and then use it locally:
1. Clone the directory: `git clone https://github.com/SynBioDex/Excel-to-SBOL`
2. Change to the excel2sbol folder:
cd ./Excel_to_SBOL/excel2sbol
3. Install an editable version of the package: `python -m pip install -e .` (will overwrite the directory in site-packages with a symbolic link to the locations repository). If a virtual environment is being used the python -m can be left off.