FAIRsoft 0.1.15

FAIRsoft package for the aggregation of Life Sciences software metadata and FAIR evaluation.

FAIRsoft

Library for the aggregation of Life Sciences software metadata and FAIR evaluation.

Installation

Install using pip:

pip install FAIRsoft

Requirements

In order to use the Bioconda and repositories (GitHub and Bitbucket) metadata importers, the following tools need to be installed:

• bioconda-utils is required by the bioconda importer.

  bioconda-utils is a bioconda package and thus requires Conda.

  ❗️ The large size of bioconda-utils package can cause Conda to crash during the installation process. Using Mamba instead of Conda prevents this problem.

  ❗️ bioconda-utils requires Python 3.7 or lower. Simulating a compatible platform might be necessary. To do so, use the following commands:

  # create the environment
  mamba create -n myenv
  
  # activate the environment
  conda activate myenv
  
  # before installing anything in the environment, set the usage of x86_64 architecture
  conda config --env --set subdir osx-64
  

• opeb-enrichers/repoEnricher is required by the Source Code Respositories importer.

• AnyStyle is required by the Galaxy Toolshed importer.

Usage

Data extraction

Configuration of the importers is done through environment variables. The following table shows the available configuration options for each importer.

Name	Description	Default	Notes
HOST	Host of database where output will be pushed	localhost
PORT	Port of database where output will be pushed	27017
DB	Name of database where output will be pushed	observatory
ALAMBIQUE	Name of database where output will be pushed	alambique
RECIPES_PATH	Path to bioconda recipes (from repository)	./bioconda-recipes/recipes	Only required when running natively AND if the location of bioconda recipes changes
GALAXY_METADATA	Path to metadata extracted from Galaxy Metadata. This JSON file, automatically generated after the extraction of repositories metadata, constains identifiers that are necessary for the download of repositories, which contain the recipes.	./data/galaxy_metadata.json
URL_SOURCEFORGE_PACKAGES	URL to SourceForge packages of our interest	https://sourceforge.net/directory/science-engineering/bioinformatics/
PACKAGES_URLS_PATH	Path to file containing the URLs of the bioconductor packages to be scraped.	./data/bioconductor_opeb.txt
REPOENRICHER_PATH	Path to repoEnricher program main file (repoEnricher.pl)	./opeb-enrichers/repoEnricher/repoEnricher.pl	Only required when running natively AND if the location of repoEnricher/ changes
REPOENRICHER_CONFIG_PATH	Path to repoEnricher configuration file	./opeb-enrichers/repoEnricher/config.ini
REPOENRICHER_OUTPUT_PATH	Path to repoEnricher output files	./data/output
URL_OPEB_TOOLS	URL to OpenEBench Tools API	https://openebench.bsc.es/monitor/tool
URL_OPEB_METRICS	URL to OpenEBench Metrics API	https://openebench.bsc.es/monitor/metrics/

An example of how to do so is shown below in run_importations.py.

Data transformation

Execute the following command to transform the data:

FAIRsoft_transform --env-file .env -l=DEBUG

Data integration

Execute the following command to integrate the data:

FAIRsoft_integrate --env-file .env