"""Set up fixtures for tests"""
import io
import os
import uuid
import shutil
from pathlib import Path
from hashlib import sha256
import redis
import pytest
import jsonpickle
from redis import Redis
from functional_tools import take
from uploader import jobs, create_app
from uploader.jobs import JOBS_PREFIX
from quality_control.errors import InvalidValue, DuplicateHeading
@pytest.fixture(scope="session")
def strains():
"""Parse the strains once every test session"""
stainnames = set()
with open("etc/strains.csv", encoding="utf8") as strains_file:
for idx, line in enumerate(strains_file.readlines()):
if idx > 0:
parts = line.split()
for name in (parts[1], parts[2]):
stainnames.add(name.strip())
if len(parts) >= 6:
alias = parts[5].strip()
if alias != "" and alias not in ("P", "\\N"):
stainnames.add(alias)
return tuple(stainnames)
def cleanup_redis(redisuri: str, prefix: str):
"""Delete all keys with given prefix"""
with Redis.from_url(redisuri, decode_responses=True) as rconn:
cur = rconn.scan_iter(f"{prefix}:*")
while True:
batch = take(cur, 500)
if len(batch) <= 0:
break
rconn.delete(*batch)
@pytest.fixture(scope="module")
def client():
"Fixture for test client"
test_prefix = sha256(f"test:{uuid.uuid4()}".encode("utf8")).hexdigest()
tests_work_dir = Path("/tmp/{test_prefix}")
tests_work_dir.mkdir(exist_ok=True)
app = create_app({
"TESTING": True,
"GNQC_REDIS_PREFIX": f"{test_prefix}:GNQC",
"JOBS_TTL_SECONDS": 2 * 60 * 60,# 2 hours
"ASYNCHRONOUS_JOBS_SQLITE_DB": f"{tests_work_dir}/jobs.db"
})
with app.app_context():
yield app.test_client()
cleanup_redis(app.config["REDIS_URL"], test_prefix)
shutil.rmtree(tests_work_dir, ignore_errors=True)
@pytest.fixture(scope="module")
def db_url(client):#pylint: disable=[redefined-outer-name]
"""Return the database URI"""
return client.application.config["SQL_URI"]
@pytest.fixture(scope="module")
def redis_url(client):#pylint: disable=[redefined-outer-name]
"""Return the redis URI"""
return client.application.config["REDIS_URL"]
@pytest.fixture(scope="module")
def redis_prefix(client):#pylint: disable=[redefined-outer-name]
"""Return the redis prefix"""
return client.application.config["GNQC_REDIS_PREFIX"]
@pytest.fixture(scope="module")
def jobs_prefix(redis_prefix):#pylint: disable=[redefined-outer-name]
"""Return the redis prefix for jobs."""
return f"{redis_prefix}:{JOBS_PREFIX}"
@pytest.fixture(scope="module")
def redis_ttl(client):#pylint: disable=[redefined-outer-name]
"""Return the redis URI"""
return client.application.config["JOBS_TTL_SECONDS"]
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"
def cleanup_job(rconn, jobid, thejob):
"""Delete job from redis."""
rconn.hdel(jobs.job_key(jobs.jobsnamespace(), jobid), *thejob.keys())
rconn.delete(jobs.job_key(jobs.jobsnamespace(), jobid))
@pytest.fixture(scope="function")
def redis_conn_with_fresh_job(redis_url, redis_ttl, jobs_prefix, job_id):#pylint: disable=[redefined-outer-name]
"redis connection with fresh, unprocessed job"
thejob = {
"jobid": job_id, "command": "some_test_command", "job_type": "testjob",
"ttl_seconds": redis_ttl, "rprefix": jobs_prefix, "extra_meta": {
"filename": "/path/to/some/file.tsv", "percent": 0,
"status": "pending"}}
with redis.Redis.from_url(redis_url, decode_responses=True) as rconn:
jobs.initialise_job(rconn, **thejob)
yield rconn
cleanup_job(rconn, job_id, thejob)
@pytest.fixture(scope="function")
def redis_conn_with_in_progress_job_no_errors(redis_url, redis_ttl, jobs_prefix, job_id):#pylint: disable=[redefined-outer-name]
"redis connection with partially processed job, with no errors"
thejob = {
"jobid": job_id, "command": "some_test_command",
"ttl_seconds": redis_ttl, "rprefix": jobs_prefix, "job_type": "testjob",
"extra_meta": {
"status": "Processing", "filename": "/path/to/some/file.tsv",
"percent": 32.242342}}
with redis.Redis.from_url(redis_url, decode_responses=True) as rconn:
jobs.initialise_job(rconn, **thejob)
yield rconn
cleanup_job(rconn, job_id, thejob)
@pytest.fixture(scope="function")
def redis_conn_with_in_progress_job_some_errors(redis_url, redis_ttl, jobs_prefix, job_id): # pylint: disable=[redefined-outer-name]
"redis connection with partially processed job, with some errors"
the_job = {
"jobid": job_id, "command": "some_test_command",
"ttl_seconds": redis_ttl, "rprefix": jobs_prefix, "job_type": "testjob",
"extra_meta": {
"status": "Processing", "filename": "/path/to/some/file.tsv",
"percent": 45.34245, "errors": jsonpickle.encode((
DuplicateHeading(
"__test__", 1, (5,13,19), "DupHead", "Heading 'DupHead' is repeated"),
InvalidValue("__test__", 45, 2, "ohMy", "Invalid value 'ohMy'")))}
}
with redis.Redis.from_url(redis_url, decode_responses=True) as rconn:
jobs.initialise_job(rconn, **the_job)
yield rconn
cleanup_job(rconn, job_id, the_job)
@pytest.fixture(scope="function")
def redis_conn_with_completed_job_no_errors(redis_url, redis_ttl, jobs_prefix, job_id): # pylint: disable=[redefined-outer-name]
"redis connection with completely processed job, with no errors"
the_job = {
"jobid": job_id, "command": ["complete", "--woerror", "test-command"],
"ttl_seconds": redis_ttl, "rprefix": jobs_prefix, "job_type": "testjob",
"extra_meta": {
"status": "success", "filename": "/path/to/some/file.tsv",
"percent": 100, "errors": jsonpickle.encode(tuple())}}
with redis.Redis.from_url(redis_url, decode_responses=True) as rconn:
jobs.initialise_job(rconn, **the_job)
yield rconn
cleanup_job(rconn, job_id, the_job)
@pytest.fixture(scope="function")
def redis_conn_with_completed_job_some_errors(redis_url, redis_ttl, jobs_prefix, job_id): # pylint: disable=[redefined-outer-name]
"redis connection with completely processed job, with some errors"
the_job = {
"jobid": job_id, "command": ["complete", "--werror", "test-command"],
"ttl_seconds": redis_ttl, "rprefix": jobs_prefix, "job_type": "testjob",
"extra_meta": {
"status": "success", "filename": "/path/to/some/file.tsv",
"percent": 100, "errors": jsonpickle.encode((
DuplicateHeading(
"__test__", 1, (5,13,19), "DupHead", "Heading 'DupHead' is repeated"),
InvalidValue("__test__", 45, 2, "ohMy", "Invalid value 'ohMy'")))}}
with redis.Redis.from_url(redis_url, decode_responses=True) as rconn:
jobs.initialise_job(rconn, **the_job)
yield rconn
cleanup_job(rconn, job_id, the_job)
@pytest.fixture(scope="function")
def uploads_dir(client): # pylint: disable=[redefined-outer-name]
"""Returns the configured, uploads directory, creating it if it does not
exist."""
the_dir = client.application.config["UPLOAD_FOLDER"]
if not os.path.exists(the_dir):
os.mkdir(the_dir)
return the_dir
@pytest.fixture(scope="function")
def jobs_errors_dir(uploads_dir): # pylint: disable=[redefined-outer-name]
"""Returns the configured, jobs errors directory, creating it if it does not
exist."""
the_dir = f"{uploads_dir}/job_errors"
if not os.path.exists(the_dir):
os.mkdir(the_dir)
return the_dir
@pytest.fixture(scope="function")
def stderr_with_output(jobs_errors_dir, job_id): # pylint: disable=[redefined-outer-name]
"""Creates a sample worker error file with some content"""
filepath = f"{jobs_errors_dir}/job_{job_id}.error"
with open(filepath, "w", encoding="utf8") as error_file:
error_file.write("This is an non-empty error file.")
error_file.flush()
yield filepath
os.remove(filepath)
@pytest.fixture(scope="function")
def stderr_with_no_output(jobs_errors_dir, job_id): # pylint: disable=[redefined-outer-name]
"""Creates a sample worker error file with no content"""
filepath = f"{jobs_errors_dir}/job_{job_id}.error"
with open(filepath, "w", encoding="utf-8") as error_file:
error_file.flush()
yield filepath
os.remove(filepath)
