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P3 API Testing Overview

Running P3 API Locally with Local Solr

  1. Install Solr. Follow steps in the patric_solr repo here.

  2. Start Solr. Note: It will probably be necessary for testing to allocate at least a couple GB to the JVM as follows.

./bin/solr restart -m 2048m -Dsolr.solr.home=<full_path_to_patric_solr> -Dlucene.version=5.3
  1. Start Redis.
redis-server
  1. Start p3_api using npm start, or
pm2 start app.js -i 3 --name "p3_api" --merge-logs -o p3_api_service.out.log -e p3_api_service.err.log

If the API is configured properly, http://localhost:3001/health should return "OK" with 200 status.

Loading test data

Recommended:
  1. The following will download 50 'exemplary' genomes to ./test-files and then index them at the provided endpoint using the -e, --endpoint option.
./load-test-solr.js -e http://localhost:8983/solr -g ./50-test-genome-ids.json -f ./test-files-public
  1. Meanwhile, you can download/index a second second set of 50 genomes, and also set the owner to be a test user with the -o, --owner option.
./load-test-solr.js -o [email protected] -e http://localhost:8983/solr -g ./50-test-genome-ids-2.json -f ./test-files-private --set-private

Some other scripts/examples:

Fetch 20 genomes (and associated cores for each) and write JSON

./generate-local-data-files.js --bulk=20 --output="./data-files"

Given a directory of genomes related files in ./test-files/...

├── 86662.6/ │ ├── genome.json │ ├── genome_amr.json │ ├── genome_feature.json │ ├── genome_sequence.json │ ├── pathway.json │ ├── sp_gene.json │ └── subsystem.json ├── 872325.3/ │ ├── genome.json ...

...index them into Solr and set the "owner" fields:

./index-local-data-files.js -i ./test-files/ -e http://localhost:8983/some/solr [email protected]

Running Tests.

The following is an example of running permission tests using Mocha/Chai.

  1. Copy tests/config.sample.json to tests/config.json and add test token accordingly.

  2. Run!

npm run test-permissions

If successful, the resulting output will look something like this:

  Test Genome Permissions
    ✓ should return 404 without genome id (231ms)
    add new permissions (user1 with read and user2 with write)
      ✓ should return 200 with "OK" (6050ms)
      ✓ should have correct permissions on genome core (659ms)
    remove all permissions
      ✓ should return 200 with "OK" (6198ms)
      ✓ should have no permissions on genome core (167ms)
    test bad inputs
      ✓ should give 401 without token
      ✓ should give 401 if bogus token (201ms)
      ✓ should give 403 if not owner (197ms)
      ✓ should return 200 for invalid input (6296ms)
    ...

Adding Tests

More sets of tests can be added following the structure in tests/.