igs-toolbox

Description

This Python package contains tools to check whether files follow predefined schemas of the IGS project. Currently, only a JSON validator is implemented, but the idea is that it will be extended to more applications related to the IGS project in the future.

Installation

igs-toolbox is installable using pip.

pip install igs-toolbox

Usage

All tools can be used directly through the commandline.

jsonChecker

usage: jsonChecker [-h] -i INPUT 

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Filepath to json file.

convertSeqMetadata

The method to convert the metadata table into JSONs for each sample. This inlcudes a validation to check if the IGS metadata scheme is matched.

Usage: convertSeqMetadata [OPTIONS]

  Convert table of seq metadata to json files.

Options:
  -i, --input FILE                Path to input excel or csv/tsv file.
                                  [required]
  -o, --output DIRECTORY          Path to output folder for json files.
                                  [required]
  -l, --log_file FILE             Path to log file.  [default:
                                  convertSeqMetadata_2023-12-01T09-56-04.log]
  --version
  --install-completion [bash|zsh|fish|powershell|pwsh]
                                  Install completion for the specified shell.
  --show-completion [bash|zsh|fish|powershell|pwsh]
                                  Show completion for the specified shell, to
                                  copy it or customize the installation.
  --help                          Show this message and exit.

Example:

convertSeqMetadata -i IGS_Metadata.xlsx -o out/

readQR

The method readQR reads the Meldungsquittung and extracts the MeldungsID.

Poppler is required to read the pdfs

conda install poppler
or
mamba install poppler
or
apt install poppler-utils

usage: readQR [-h] [--version] [file ...]

positional arguments:
  file

options:
  -h, --help  show this help message and exit
  --version   show program's version number and exit

Example:

readQR *.pdf