Commit a7433e70 authored by Cage, Gregory's avatar Cage, Gregory
Browse files

Merge branch '17-initial-testing' into 'main' 

Add initial testing for library

Closes #17

See merge request ndip/public-packages/nova-galaxy!3
parents 112b0973 d08e8652

.gitlab-ci.yml

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@@ -8,6 +8,8 @@ variables: 
  GIT_STRATEGY: clone

  IMAGE_NAME: ${NDIP_DOCKER_REPOSITORY}/${CI_PROJECT_PATH}

  IMAGE_TAG: "0.1.0"

  GALAXY_URL: "https://calvera-test.ornl.gov"

  GALAXY_KEY: ${SERVICE_ACCOUNT_API_KEY}



before_script:

  - curl https://code.ornl.gov/rse-deployment/rse-sharables/raw/master/rse-bash-modules.sh -O
@@ -36,9 +38,9 @@ unit-tests: 
  stage: test

  script:

    - mkdir reports

    - docker run -u `id -u`:`id -g` -v `pwd`/reports:/src/reports ${IMAGE_NAME}:src-${CI_COMMIT_SHA} poetry run coverage run

    - docker run -u `id -u`:`id -g` -v `pwd`/reports:/src/reports ${IMAGE_NAME}:src-${CI_COMMIT_SHA} poetry run coverage report

    - docker run -u `id -u`:`id -g` -v `pwd`/reports:/src/reports ${IMAGE_NAME}:src-${CI_COMMIT_SHA} poetry run coverage xml -o reports/coverage.xml

    - docker run -u `id -u`:`id -g` -v `pwd`/reports:/src/reports -e NOVA_GALAXY_TEST_GALAXY_KEY=${GALAXY_KEY} -e NOVA_GALAXY_TEST_GALAXY_URL=${GALAXY_URL} ${IMAGE_NAME}:src-${CI_COMMIT_SHA} poetry run coverage run

    - docker run -u `id -u`:`id -g` -v `pwd`/reports:/src/reports -e NOVA_GALAXY_TEST_GALAXY_KEY=${GALAXY_KEY} -e NOVA_GALAXY_TEST_GALAXY_URL=${GALAXY_URL} ${IMAGE_NAME}:src-${CI_COMMIT_SHA} poetry run coverage report

    - docker run -u `id -u`:`id -g` -v `pwd`/reports:/src/reports -e NOVA_GALAXY_TEST_GALAXY_KEY=${GALAXY_KEY} -e NOVA_GALAXY_TEST_GALAXY_URL=${GALAXY_URL} ${IMAGE_NAME}:src-${CI_COMMIT_SHA} poetry run coverage xml -o reports/coverage.xml

    - sed -i "s:<source>/src:<source>${CI_BUILDS_DIR}/${CI_PROJECT_PATH}:" reports/coverage.xml



  coverage: '/TOTAL.*? (100(?:\.0+)?\%|[1-9]?\d(?:\.\d+)?\%)$/'

README.md

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@@ -32,10 +32,14 @@ poetry run mypy . 
```



## Testing

You can run the tests for this package with the following command from the base directory:

```commandline

poetry run pytest

NOVA_GALAXY_TEST_GALAXY_URL=galaxy-url NOVA_GALAXY_TEST_GALAXY_KEY=key poetry run pytest tests/

```

or, with coverage

with `NOVA_GALAXY_TEST_GALAXY_URL` being the url of your Galaxy instance and `NOVA_GALAXY_TEST_GALAXY_KEY` being your

Galaxy API Key.



To run tests with coverage (include the above environment variables):

```commandline

poetry run coverage run

poetry run coverage report

src/nova/galaxy/tool.py

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"""Contains classes to run tools in Galaxy via Nova."""



import time

from typing import List, Union

from typing import List, Optional, Union



from bioblend import galaxy
@@ -77,7 +77,9 @@ class Tool(AbstractWork): 


        return outputs



    def run_interactive(self, data_store: Datastore, params: Parameters, max_tries: int = 100) -> str:

    def run_interactive(

        self, data_store: Datastore, params: Parameters, max_tries: int = 100, check_url: bool = True

    ) -> Optional[str]:

        galaxy_instance = data_store.nova_connection.galaxy_instance

        datasets_to_upload = {}

        # Set Tool Inputs
@@ -107,7 +109,7 @@ class Tool(AbstractWork): 
                if ep["job_id"] == job_id and ep.get("target", None):

                    url = f"{data_store.nova_connection.galaxy_url}{ep['target']}"

                    response = galaxy_instance.make_get_request(url)

                    if response.status_code == 200:

                    if response.status_code == 200 or not check_url:

                        return url

            timer -= 1

            time.sleep(1)

tests/conftest.py

0 → 100644
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"""Config for testing."""



import os



import pytest

from bioblend.galaxy import GalaxyInstance



from nova.galaxy.nova import Nova



GALAXY_URL = os.environ.get("NOVA_GALAXY_TEST_GALAXY_URL", "https://calvera-test.ornl.gov")

GALAXY_API_KEY = os.environ.get("NOVA_GALAXY_TEST_GALAXY_KEY")





@pytest.fixture

def nova_instance() -> Nova:

    nova = Nova(GALAXY_URL, GALAXY_API_KEY)

    return nova





@pytest.fixture

def galaxy_instance() -> GalaxyInstance:

    galaxy = GalaxyInstance(url=GALAXY_URL, key=GALAXY_API_KEY)

    return galaxy

tests/test_data_store.py

0 → 100644
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"""Tests for data stores."""



from bioblend.galaxy import GalaxyInstance



from nova.galaxy.nova import Nova





def test_no_persist_store(nova_instance: Nova, galaxy_instance: GalaxyInstance) -> None:

    with nova_instance.connect() as connection:

        store = connection.create_data_store(name="nova_galaxy_testing")

        history = galaxy_instance.histories.get_histories(name=store.name)

        assert len(history) > 0

    history = galaxy_instance.histories.get_histories(name=store.history_id, deleted=False)

    assert len(history) < 1





def test_persist_store(nova_instance: Nova, galaxy_instance: GalaxyInstance) -> None:

    with nova_instance.connect() as connection:

        store = connection.create_data_store(name="nova_galaxy_testing")

        store.persist()

        history = galaxy_instance.histories.get_histories(name=store.name)

        assert len(history) > 0

    history = galaxy_instance.histories.get_histories(name=store.name, deleted=False)

    assert len(history) > 0

    # TODO: Can maybe do global cleanup

    galaxy_instance.histories.delete_history(history_id=history[0]["id"], purge=True)