sckan-composer

Prerequisites

Python

The deployment process is based on Python 3.9+ scripts. It is recommended to setup a virtual environment first.

With venv:

python3 -m venv venv
source venv/bin/activate

With pyenv (get it here):

pyenv virtualenv 3.9.15 composer
pyenv activate composer

With (mini)conda (get it here):

conda create --name composer python=3.9
conda activate composer

Development setup

Running locally

cd backend
# make sure your virtual env is activated
# and install the requirements
pip3 install --upgrade -r requirements.txt
# run the migrations
python3 manage.py migrate
# run the development server (https)
python3 manage.py runsslserver

Ingest sample NLP data

The git repository comes with some sample NLP data. This data can be ingested using the "ingest_nlp_sentence" management command

cd applications/composer/backend
python3 manage.py ingest_nlp_sentence ./composer/resources/pmc_oai_202209.csv

Ingest sample Anatomical Entities data

The git repository comes with some sampleAnatomical Entities data. This data can be ingested using the "ingest_anatomical_entities" management command

cd applications/composer/backend
python3 manage.py ingest_anatomical_entities ./composer/resources/anatomical_entities.csv

Ingest Statements

You can get the detailed shell script at - backend/run_ingest.sh

python manage.py ingest_statements --update_upstream

You can add custom full imports and label imports to the above command by using the flags --full_imports and --label_imports respectively. Example below:

python manage.py ingest_statements --update_upstream --full_imports apinat-partial-orders apinat-pops-more sparc-nlp --label_imports apinatomy-neuron-populations ../../npo

here - apinat-partial-orders and apinat-pops-more sparc-nlp are the full imports and apinatomy-neuron-populations and ../../npo are the label imports.

NOTE: full imports are done from https://raw.githubusercontent.com/SciCrunch/NIF-Ontology/neurons/ttl/generated/neurons/*.ttl and label imports are done from https://raw.githubusercontent.com/SciCrunch/NIF-Ontology/neurons/ttl/generated/neurons/*.ttl, and if you want a different path, you can use it relatively like - ../../npo

Ingest Statement's Curie ID

You can run the following command to ingest the curie id for the statements

python manage.py update_connectivity_statement_field--cs_field curie_id --neurondm_field label

Open the admin page

there will be a superuser created with username/password: admin/admin

browse the Django admin interface

Install openapi generator

For generating the frontend api client use the openapi generator install:

npm install -g @openapitools/openapi-generator-cli

and then run

cd frontend
./genapi.sh

ORCID login setup

browse to ORCID dev tools and create a new api configure settings.py with the new key and secret