diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/conftest.py | 83 | ||||
| -rw-r--r-- | tests/qc_app/test_parse.py | 15 | ||||
| -rw-r--r-- | tests/qc_app/test_progress_indication.py | 109 |
3 files changed, 198 insertions, 9 deletions
diff --git a/tests/conftest.py b/tests/conftest.py index 9755a47..90d8264 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -5,10 +5,13 @@ import socket import subprocess from contextlib import closing +import redis import pytest +import jsonpickle from qc_app import create_app from quality_control.parsing import strain_names +from quality_control.errors import InvalidValue, DuplicateHeading @pytest.fixture(scope="session") def strains(): @@ -44,3 +47,83 @@ def uploadable_file_object(filename): "Return an 'object' representing the file to be uploaded." with open(f"tests/test_data/{filename}", "br") as the_file: return (io.BytesIO(the_file.read()), filename) + +@pytest.fixture(scope="function") +def job_id(): + "Return a default UUID4 string as the 'job_id' for test purposes" + return "934c55d8-396e-4959-90e1-2698e9205758" + +@pytest.fixture(scope="function") +def redis_conn_with_fresh_job(redis_url, job_id): # pylint: disable=[redefined-outer-name] + "redis connection with fresh, unprocessed job" + the_job = { + "job_id": job_id, "command": "some_test_command", "status": "pending", + "filename": "/path/to/some/file.tsv", "percent": 0 + } + with redis.Redis.from_url(redis_url, decode_responses=True) as rconn: + rconn.hset(name=job_id, mapping=the_job) + yield rconn + rconn.hdel(job_id, *the_job.keys()) + rconn.delete(job_id) + +@pytest.fixture(scope="function") +def redis_conn_with_in_progress_job_no_errors(redis_url, job_id): # pylint: disable=[redefined-outer-name] + "redis connection with partially processed job, with no errors" + the_job = { + "job_id": job_id, "command": "some_test_command", + "status": "Processing", "filename": "/path/to/some/file.tsv", + "percent": 32.242342 + } + with redis.Redis.from_url(redis_url, decode_responses=True) as rconn: + rconn.hset(name=job_id, mapping=the_job) + yield rconn + rconn.hdel(job_id, *the_job.keys()) + rconn.delete(job_id) + +@pytest.fixture(scope="function") +def redis_conn_with_in_progress_job_some_errors(redis_url, job_id): # pylint: disable=[redefined-outer-name] + "redis connection with partially processed job, with some errors" + the_job = { + "job_id": job_id, "command": "some_test_command", + "status": "Processing", "filename": "/path/to/some/file.tsv", + "percent": 45.34245, "errors": jsonpickle.encode(( + DuplicateHeading( + 1, (5,13,19), "DupHead", "Heading 'DupHead' is repeated"), + InvalidValue(45, 2, "ohMy", "Invalid value 'ohMy'"))) + } + with redis.Redis.from_url(redis_url, decode_responses=True) as rconn: + rconn.hset(name=job_id, mapping=the_job) + yield rconn + rconn.hdel(job_id, *the_job.keys()) + rconn.delete(job_id) + +@pytest.fixture(scope="function") +def redis_conn_with_completed_job_no_errors(redis_url, job_id): # pylint: disable=[redefined-outer-name] + "redis connection with completely processed job, with no errors" + the_job = { + "job_id": job_id, "command": "some_test_command", + "status": "success", "filename": "/path/to/some/file.tsv", + "percent": 100 + } + with redis.Redis.from_url(redis_url, decode_responses=True) as rconn: + rconn.hset(name=job_id, mapping=the_job) + yield rconn + rconn.hdel(job_id, *the_job.keys()) + rconn.delete(job_id) + +@pytest.fixture(scope="function") +def redis_conn_with_completed_job_some_errors(redis_url, job_id): # pylint: disable=[redefined-outer-name] + "redis connection with completely processed job, with some errors" + the_job = { + "job_id": job_id, "command": "some_test_command", + "status": "success", "filename": "/path/to/some/file.tsv", + "percent": 100, "errors": jsonpickle.encode(( + DuplicateHeading( + 1, (5,13,19), "DupHead", "Heading 'DupHead' is repeated"), + InvalidValue(45, 2, "ohMy", "Invalid value 'ohMy'"))) + } + with redis.Redis.from_url(redis_url, decode_responses=True) as rconn: + rconn.hset(name=job_id, mapping=the_job) + yield rconn + rconn.hdel(job_id, *the_job.keys()) + rconn.delete(job_id) diff --git a/tests/qc_app/test_parse.py b/tests/qc_app/test_parse.py index 46b45d9..a4bfdd5 100644 --- a/tests/qc_app/test_parse.py +++ b/tests/qc_app/test_parse.py @@ -6,11 +6,8 @@ import pytest from qc_app.jobs import job from tests.conftest import uploadable_file_object -def module_uuid4(): - "module patch for the `uuid.uuid4()` function" - return "934c55d8-396e-4959-90e1-2698e9205758" - -def test_parse_with_existing_uploaded_file(client, redis_url, monkeypatch): +def test_parse_with_existing_uploaded_file( + client, redis_url, job_id, monkeypatch): """ GIVEN: 1. A flask application testing client 2. A valid file, and filetype @@ -19,7 +16,7 @@ def test_parse_with_existing_uploaded_file(client, redis_url, monkeypatch): 1. the system redirects to the job/parse status page 2. the job is placed on redis for processing """ - monkeypatch.setattr("qc_app.jobs.uuid4", module_uuid4) + monkeypatch.setattr("qc_app.jobs.uuid4", lambda : job_id) # Upload a file filename = "no_data_errors.tsv" filetype = "average" @@ -34,14 +31,14 @@ def test_parse_with_existing_uploaded_file(client, redis_url, monkeypatch): assert b'/parse/status/934c55d8-396e-4959-90e1-2698e9205758' in resp.data with redis.Redis.from_url(redis_url, decode_responses=True) as rconn: - the_job = job(rconn, module_uuid4()) + the_job = job(rconn, job_id) - assert the_job["job_id"] == module_uuid4() + assert the_job["job_id"] == job_id assert the_job["filename"] == filename assert the_job["command"] == " ".join([ "python3", "-m", "scripts.worker", filetype, f"{client.application.config['UPLOAD_FOLDER']}/{filename}", redis_url, - module_uuid4()]) + job_id]) @pytest.mark.parametrize( "filename,uri,error_msgs", diff --git a/tests/qc_app/test_progress_indication.py b/tests/qc_app/test_progress_indication.py new file mode 100644 index 0000000..11a412e --- /dev/null +++ b/tests/qc_app/test_progress_indication.py @@ -0,0 +1,109 @@ +"Test that the progress indication works correctly" + +def test_with_non_existing_job(client, redis_conn_with_fresh_job): # pylint: disable=[unused-argument] + """ + GIVEN: 1. A flask application testing client + 2. A redis instance with a fresh, unstarted job + WHEN: The parsing progress page is loaded for a non existing job + THEN: Ensure that the page: + 1. Has a meta tag to redirect it to the index page after 5 seconds + 2. Has text indicating that the job does not exist + """ + job_id = "non-existent-job-id" + resp = client.get(f"/parse/status/{job_id}") + assert resp.status_code == 400 + assert ( + b"No job, with the id '<em>non-existent-job-id</em>' was found!" + in resp.data) + assert b'<meta http-equiv="refresh" content="5;url=/">' in resp.data + +def test_with_unstarted_job(client, job_id, redis_conn_with_fresh_job): # pylint: disable=[unused-argument] + """ + GIVEN: 1. A flask application testing client + 2. A redis instance with a fresh, unstarted job + WHEN: The parsing progress page is loaded + THEN: Ensure that the page: + 1. Has a meta tag to refresh it after 5 seconds + 2. Has a progress indicator with zero progress + """ + resp = client.get(f"/parse/status/{job_id}") + assert b'<meta http-equiv="refresh" content="5">' in resp.data + assert ( + b'<progress id="job_' + + (f'{job_id}').encode("utf8") + + b'" value="0.0">0.0</progress>') in resp.data + +def test_with_in_progress_no_error_job( + client, job_id, redis_conn_with_in_progress_job_no_errors): # pylint: disable=[unused-argument] + """ + GIVEN: 1. A flask application testing client + 2. A redis instance with a job in progress, with no errors found in + the file so far + WHEN: The parsing progress page is loaded + THEN: Ensure that the page: + 1. Has a meta tag to refresh it after 5 seconds + 2. Has a progress indicator with the percent of the file processed + indicated + """ + resp = client.get(f"/parse/status/{job_id}") + assert b'<meta http-equiv="refresh" content="5">' in resp.data + assert ( + b'<progress id="job_' + + (f'{job_id}').encode("utf8") + + b'" value="0.32242342">32.242342</progress>') in resp.data + assert ( + b'<span class="alert-success">No errors found so far</span>' + in resp.data) + assert b"<table" not in resp.data + +def test_with_in_progress_job_with_errors( + client, job_id, redis_conn_with_in_progress_job_some_errors): # pylint: disable=[unused-argument] + """ + GIVEN: 1. A flask application testing client + 2. A redis instance with a job in progress, with some errors found in + the file so far + WHEN: The parsing progress page is loaded + THEN: Ensure that the page: + 1. Has a meta tag to refresh it after 5 seconds + 2. Has a progress indicator with the percent of the file processed + indicated + 3. Has a table showing the errors found so far + """ + resp = client.get(f"/parse/status/{job_id}") + assert b'<meta http-equiv="refresh" content="5">' in resp.data + assert ( + b'<progress id="job_' + + (f'{job_id}').encode("utf8") + + b'" value="0.4534245">45.34245</progress>') in resp.data + assert ( + b'<p class="alert-error">We have found the following errors so far</p>' + in resp.data) + assert b'table class="reports-table">' in resp.data + assert b'Duplicate Header' in resp.data + assert b'Invalid Value' in resp.data + +def test_with_completed_job_no_errors( + client, job_id, redis_conn_with_completed_job_no_errors): # pylint: disable=[unused-argument] + """ + GIVEN: 1. A flask application testing client + 2. A redis instance with a completed job, with no errors found in + the file so far + WHEN: The parsing progress page is loaded + THEN: Ensure that the response is a redirection to the results page + """ + resp = client.get(f"/parse/status/{job_id}") + assert resp.status_code == 302 + assert f"/parse/results/{job_id}".encode("utf8") in resp.data + +def test_with_completed_job_some_errors( + client, job_id, redis_conn_with_completed_job_no_errors): # pylint: disable=[unused-argument] + """ + GIVEN: 1. A flask application testing client + 2. A redis instance with a completed job, with some errors found in + the file so far + WHEN: The parsing progress page is loaded + THEN: Ensure that the response is a redirection to the results page + """ + resp = client.get(f"/parse/status/{job_id}") + assert resp.status_code == 302 + assert f"/parse/results/{job_id}".encode("utf8") in resp.data |