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"""Set up fixtures for tests"""
import io
import os
import shutil
import socket
import subprocess
from contextlib import closing
import redis
import pytest
import jsonpickle
from qc_app import create_app
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 is_port_in_use(port: int) -> bool:
"Check whether `port` is in use"
with closing(socket.socket(socket.AF_INET, socket.SOCK_STREAM)) as sckt:
return sckt.connect_ex(("localhost", port)) == 0
@pytest.fixture(scope="session")
def redis_url():
"Fixture to launch a new redis instance and return appropriate URI"
port = next(# pylint: disable=[stop-iteration-return]
port for port in range(6379,65535) if not is_port_in_use(port))
command = [shutil.which("redis-server"), "--port", str(port)]
process = subprocess.Popen(command) # pylint: disable=[consider-using-with]
yield f"redis://localhost:{port}"
process.kill()
@pytest.fixture(scope="module")
def client(redis_url): # pylint: disable=[redefined-outer-name]
"Fixture for test client"
app = create_app(os.environ.get("QCAPP_INSTANCE_PATH"))
app.config.update({
"REDIS_URL": redis_url,
"TESTING": True
})
yield app.test_client()
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, "errors": jsonpickle.encode(tuple())
}
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)
@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)
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