igs-toolbox

Description

This Python package contains tools to check whether files follow predefined schemas of the IGS project.

Installation

igs-toolbox is installable using pip.

pip install igs-toolbox

Usage

All tools can be used directly through the commandline.

jsonChecker

$ jsonChecker --help
                                                                                                                                                              
 Usage: jsonChecker [OPTIONS]                                                                                                                                 
                                                                                                                                                              
 Validate metadata json.                                                                                                                                      
                                                                                                                                                              
╭─ Options ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ *  --input               -i      FILE  Path to input json file. [default: None] [required]                                                                 │
│    --dwh                               Perform validation for the dwh specification.                                                                       │
│    --log_file            -l      FILE  Path to log file. [default: jsonChecker_2025-07-02T13-17-52.log]                                                    │
│    --version             -V                                                                                                                                │
│    --install-completion                Install completion for the current shell.                                                                           │
│    --show-completion                   Show completion for the current shell, to copy it or customize the installation.                                    │
│    --help                              Show this message and exit.                                                                                         │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

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.

$ convertSeqMetadata --help
                                                                                                                                                              
 Usage: convertSeqMetadata [OPTIONS]                                                                                                                          
                                                                                                                                                              
 Convert table of seq metadata to json files.                                                                                                                 
                                                                                                                                                              
╭─ Options ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ *  --input               -i      FILE       Path to input excel, csv/tsv or json file. [default: None] [required]                                          │
│ *  --output              -o      DIRECTORY  Path to output folder for json files. It will use the lab_sequence_id as filename, otherwise the input         │
│                                             filename _ row number.                                                                                         │
│                                             [default: None]                                                                                                │
│                                             [required]                                                                                                     │
│    --dwh                                    Convert input to match the IGSDWH (v3.2.0) specification.                                                      │
│    --skip-validation                        Skip all validations, this can generate invalid JSON metadata files.                                           │
│    --fix                                    Apply data fixes whenever possible.                                                                            │
│    --remove-extra                           Remove extra properties not present in the specification, requires --fix option enabled.                       │
│    --log_file            -l      FILE       Path to log file. [default: convertSeqMetadata_2025-07-02T13-15-22.log]                                        │
│    --version             -V                                                                                                                                │
│    --install-completion                     Install completion for the current shell.                                                                      │
│    --show-completion                        Show completion for the current 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

$ readQR --help
                                                                                                                                                              
 Usage: readQR [OPTIONS] INPUT_FILES...                                                                                                                       
                                                                                                                                                              
 Extract QR codes from files.                                                                                                                                 
                                                                                                                                                              
╭─ Arguments ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ *    input_files      INPUT_FILES...  Paths to input files. [default: None] [required]                                                                     │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --version             -V                                                                                                                                   │
│ --install-completion            Install completion for the current shell.                                                                                  │
│ --show-completion               Show completion for the current shell, to copy it or customize the installation.                                           │
│ --help                          Show this message and exit.                                                                                                │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

Example:

readQR *.pdf