OtoN_Converter

Converter from basic OCR-D process workflow (.txt) to Nextflow workflow script (.nf)

1. Installation of OtoN from source

1. Clone specific tag of the repository and enter it:

   git clone -b v1.1.1 git@github.com:MehmedGIT/OtoN_Converter.git
   cd OtoN_Converter

2. Create a new python virtual environment and activate it:

   python3 -m venv ~/venv-oton
   source ~/venv-oton/bin/activate

3. Install OtoN converter

   pip3 install .

2. Example conversions

1. Validation of an OCR-D process workflow txt:

   oton validate -I ./oton/assets/workflow1.txt

2. Conversion of an OCR-D process workflow txt to Nextflow workflow script:

   2.1 Native format of the Nextflow script

   oton convert -I ./oton/assets/workflow1.txt -O ./oton/assets/nextflow1.nf

   2.2 Dockerized format of the Nextflow script

   oton convert -I ./oton/assets/workflow1.txt -O ./oton/assets/nextflow1_dockerized.nf -D

3. Additional requirements (Optional)

For executing the produced Nextflow scripts there are additional requirements

1. Nextflow. Check the installation guide here. Simple installation:

   wget -qO- https://get.nextflow.io | bash
   chmod +x nextflow
   mv nextflow /usr/local/bin/
   nextflow -v

2. OCR-D ALL software for running the produced Nextflow workflows. Either installed locally or having the Docker image.

   1. Installed locally - Check the installation guide here.
   2. Docker image - Check the guide here. Or simply do:

      docker pull ocrd/all:maximum

4. Required configurations

Before proceeding to the next step 5. Example demo there are few requirements that need to be fulfilled:

4.1 Case: OCR-D installed natively

Make sure the OCR-D processors are callable from the shell. For this, the bin path of the python virtual environment where the OCR-D all software is installed has to be available in PATH. There are many ways to achieve that, but the suggested way is to extend the $PATH inside the ~/.profile, ~/.bash_profile, or ~/.bash_login.

For example, if the path to bin is: $HOME/venv37-ocrd/bin. Append the following lines to either of the 3 files above.

if [ -d "$HOME/venv37-ocrd/bin" ] ; then
    PATH="$HOME/venv37-ocrd/bin:$PATH"
fi

4.2 Case: OCR-D docker image:

4.2.1 Download/Prepare OCR-D models to volume map them to the desired location on your system:

For example, /home/mm/ocrd_models.

docker run --rm -v "/home/mm/ocrd_models/:/usr/local/share/ocrd-resources" -- ocrd/all:maximum ocrd resmgr download '*'
docker run --rm -v "/home/mm/ocrd_models/:/usr/local/share/" -- ocrd/all:maximum ocrd resmgr download ocrd-tesserocr-recognize '*'

The selected path has to be passed as an argument to the Nextflow script. Check 6. Nextflow script parameters. Also check the Nextflow script example with passed docker parameters here.

5. Example demo

1. Prepare the dummy workspace and workflow assets:

   ./prepare.sh

2. Run either of the available examples:

   2.1 Run the native example (requires Nextflow and OCR-D all local installation)

   ./run_nextflow_native.sh

   The Nextflow script executes native calls to the specified OCR-D processors

   2.2 Run the docker example (requires Nextflow and OCR-D all docker image)

   ./run_nextflow_docker.sh

   The Nextflow script executes docker calls to the specified OCR-D processors

3. Clean the produced files

   ./clean.sh

Currently, there are no known issues or bugs. Please report in case you find some.

6. Nextflow script parameters

• mets_path: the path to the mets file of an ocrd workspace.
• workspace_path: the workspace in which a workflow is executed.
• docker_pwd: the working directory of the Docker container. Has to match with the workspace_path
• docker_image: the docker image of ocrd_all. Preferably should be ocrd/all:maximum.
• models_path: the path to the models on your system.
• docker_models_dir: the directory to which the models are mounted in the ocrd_all docker container. This value usually is "/usr/local/share/ocrd-resources". However, some processors (e.g., ocrd-tesserocr-recognize) may not respect that path. For more information regarding the models check here.

Pass these parameters according to your needs when executing the Nextflow scripts.

Check the native call example with parameters here.

Check the docker call example with parameters here.

7. Planned extensions

1. Support options to ocrd processes (i.e., the first line of the OCR-D process workflow txt) (Check here)

2. Support Singularity calls inside the HPC environment - since Docker containers cannot be executed inside the HPC environment, the Docker containers have to be wrapped by Singularity containers.