TESTS.md

Work in progress: automated web service tests

To run them:

cd ws-tests
export PYTHONPATH={path to phylesystem-api repo}/ws-tests:$PYTHONPATH
{path to phylesystem-api repo}/ws-tests/run_tests.sh devapi.opentreeoflife.org

(It might be more convenient to copy opentreetesting.py and run_tests.sh locally, rather than refer to the phylesystem-api repo all the time.)

Substitute whatever API host you're testing for devapi.opentreeoflife.org.

Any test can be run individually:

cd ws-tests
export PYTHONPATH={path to phylesystem-api repo}/ws-tests:$PYTHONPATH
python test_basic.py host:apihost=http://devapi.opentreeoflife.org

You can test against a locally running neo4j instance:

cd ws-tests
export PYTHONPATH={path to phylesystem-api repo}/ws-tests:$PYTHONPATH
python test_basic.py host:apihost=http://localhost:7474 host:translate=true

When writing tests, the utilities in the opentreetesting.py library are available.

For more information on the test harness, see here.

Manual tests

Currently, there few automated tests for OTI. You can, however, fairly thoroughly test the performance manually. Run the following command to index the current phylesystem repo on devapi.opentreeoflife.org:

./index_current_repo.py http://devapi.opentreeoflife.org/oti http://devapi.opentreeoflife.org/api

(For a less time consuming test, try the asterales endpoint.)

And then (assuming indexing worked), query the database to test it. Here are some example queries using cURL, and their expected results.

Return a list of all studies:

curl -X POST http://devapi.opentreeoflife.org/oti/ext/studies/graphdb/find_studies

{
  "matched_studies" : [ {
    "ot:studyId" : "1354"
  }, {
    "ot:studyId" : "2189"
  }, # snipped
  {
    "ot:studyId" : "2326"
  }, {
    "ot:studyId" : "1827"
  } ]
}

Search for studies with trees spanning the taxon with name "Annona glabra":

curl -X POST http://devapi.opentreeoflife.org/oti/ext/studies/graphdb/find_trees -H "content-type: application/json" -d '{"property":"ot:ottTaxonName","value":"Annona glabra"}'

{
  "matched_studies" : [ {
    "matched_trees" : [ {
      "nexson_id" : "tree3008",
      "oti_tree_id" : "1495_tree3008"
    }, {
      "nexson_id" : "tree3009",
      "oti_tree_id" : "1495_tree3009"
    }, {
      "nexson_id" : "tree3010",
      "oti_tree_id" : "1495_tree3010"
    } ],
    "ot:studyId" : "1495"
  } ]
}

Get a list of properties available for searching studies and trees:

curl -X POST http://devapi.opentreeoflife.org/oti/ext/studies/graphdb/properties

{
  "tree_properties" : [ "ot:studyPublicationReference", "is_deprecated", "ot:focalCladeOTTTaxonName", "ot:studyLastEditor", "ot:studyModified", "ot:studyLabel", "ot:comment", "ot:studyId", "ot:dataDeposit", "ot:authorContributed", "ot:studyUploaded", "ot:studyYear", "ot:focalCladeTaxonName", "ot:tag", "ot:curatorName", "ot:studyPublication", "ot:focalCladeOTTId", "ot:focalClade" ],
  "study_properties" : [ "ot:studyPublicationReference", "is_deprecated", "ot:focalCladeOTTTaxonName", "ot:studyLastEditor", "ot:studyModified", "ot:studyLabel", "ot:comment", "ot:studyId", "ot:dataDeposit", "ot:authorContributed", "ot:studyUploaded", "ot:studyYear", "ot:focalCladeTaxonName", "ot:tag", "ot:curatorName", "ot:studyPublication", "ot:focalCladeOTTId", "ot:focalClade" ]
}