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pymnp - python API to access the MolecularNeuropathology web portal

Python API for accessing: https://www.molecularneuropathology.org/mnp/

  • Plus proxy-server with new all-sample all-status interface, allowing re-running, killing and starting new jobs (./scripts/pymnp-proxy-server.sh).
  • Plus executable downloading and caching all completed jobs (./bin/api_example_download_all.py).

pymnp

Installation & usage

git clone https://github.com/yhoogstrate/pymnp.git
cd pymnp

virtualenv -p python3 .venv
source .venv/bin/activate

pip install -r requirements.txt -U .

change to appropriate credentials:

cp config.txt.example config.txt

nano config.txt

usage web server

  1. install (see above)
  2. configure credentials (see above)
  3. run the proxy server:
virtualenv -p python 3 .venv
source .venv/bin/activate

./scripts/pymnp-proxy-server.sh
  1. go to your browser and open: http://127.0.0.1:5000/
  2. press the [update-all-data]-button
  3. press [f5]

usage downloader

  1. ensure you have completed jobs
  2. install (see above)
  3. configure credentials (see above)
  4. run the batch downloader:
virtualenv -p python 3 .venv
source .venv/bin/activate

./bin/api_example_download_all.py

ls ./cache