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HADatAc / hascoapi

Human-Aware Science Ontology API (HASCOAPI)
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HASCOAPI - Human-Aware Science Ontology API

What is HASCO?

HASCO is an ontology describing how instruments are used to acquire and collect data in support of scientific studies. The ontology has essential concepts for describing studies, study objects like subjects, instruments, instrument elements like detectors and items, instrument deployments enabling the use of instruments to acquire data, and a comprehensive semantic description of data in the context of studies and instrument deployments.

What is HASCOAPI?

It is an API for handling HASCO-based knowledge graphs. The canonical representation of instruments and instrument elements are stored in RDF inside of the Fuseki triple store embedded in HASCOAPI.

How to run HASCOAPI?

  1. HASCOAPI's host machine requires the installation of git and docker
  2. Using git clone, clone HASCOAPI from github
  3. Edit /hascoapi/conf/application.conf and replace the variable pac4.jwt.secret value with another random string of around 40 characters. This is the JWT API token that needs to be shared with the REP application (https://github.com/HADatAc/rep)
  4. Using docker build ., build HASCOAPI images
  5. Using docker-compose up -d, run HASCOAPI

How to upgrade HASCOAPI?

  1. log into HASCOAPI hosting machine
  2. Go to hascoapi folder: cd /hascoapi
  3. Bring down hascoapi containers: docker-compose down
  4. Delete current images and old containers: docker-compose system prune -a
  5. Update current code: git pull
  6. Restart hascoapi: docker-compose up -d

How to erase HASCOAPI's triplestore content?

  1. log into HASCOAPI hosting machine
  2. Go to hascoapi folder: cd /hascoapi
  3. Bring down hascoapi containers: docker-compose down
  4. Delete triplestore volume: docker volume rm hascoapi_hascoapi-fuseki-data
  5. Restart hascoapi: docker-compose up -d

How to create HASCOAPI backup file?

In the example below, we named the backup file with the backup date. This can be any date and it may also include the time of the backup.

  1. log into HASCOAPI hosting machine
  2. Go to hascoapi folder: cd /hascoapi
  3. Bring down hascoapi containers: docker-compose down
  4. Go to home folder: cd ~
  5. Generate the backup file: docker run --rm --volumes-from hascoapi_fuseki -v $PWD:/bkp ubuntu bash -c "tar -zcvf /bkp/fuseki-data_17Aug2023.tar.gz"
  6. Use sftp to copy the backup file /bkp/fuseki-data_17Aug2023.tar.gz out of the host machine

How to restore a HASCOAPI backup file?

  1. Use sftp to copy a backup file, e.g., /bkp/fuseki-data_17Aug2023.tar.gz into the HASCOAPI host machine
  2. log into HASCOAPI hosting machine
  3. Go to hascoapi folder: cd /hascoapi
  4. Bring down hascoapi containers: docker-compose down
  5. Go to home folder: cd ~
  6. Restore the backup file: docker run --rm --volumes-from hascoapi_fuseki -v $PWD:/bkp ubuntu bash -c "tar -zxvf /bkp/fuseki-data_17Aug2023.tar.gz"