Checks: Update code and tests to ensure all checks pass.

4 files changed, 60 insertions, 26 deletions

diff --git a/tests/conftest.py b/tests/conftest.py
index b7d3f8a..013c30d 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -10,7 +10,10 @@ import jsonpickle
 from redis import Redis
 
 from functional_tools import take
+
 from qc_app import jobs, create_app
+from qc_app.jobs import JOBS_PREFIX
+
 from quality_control.errors import InvalidValue, DuplicateHeading
 
 @pytest.fixture(scope="session")
@@ -56,11 +59,26 @@ def client():
     cleanup_redis(app.config["REDIS_URL"], test_prefix)
 
 @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"]
@@ -81,11 +99,11 @@ def cleanup_job(rconn, jobid, thejob):
     rconn.delete(jobs.job_key(jobs.jobsnamespace(), jobid))
 
 @pytest.fixture(scope="function")
-def redis_conn_with_fresh_job(redis_url, redis_ttl, job_id):#pylint: disable=[redefined-outer-name]
+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 = {
-        "job_id": job_id, "command": "some_test_command", "job_type": "testjob",
-        "ttl_seconds": redis_ttl, "extra_meta": {
+        "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:
@@ -94,11 +112,12 @@ def redis_conn_with_fresh_job(redis_url, redis_ttl, job_id):#pylint: disable=[re
         cleanup_job(rconn, job_id, thejob)
 
 @pytest.fixture(scope="function")
-def redis_conn_with_in_progress_job_no_errors(redis_url, redis_ttl, job_id):#pylint: disable=[redefined-outer-name]
+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 = {
-        "job_id": job_id, "command": "some_test_command",
-        "ttl_seconds": redis_ttl, "job_type": "testjob", "extra_meta": {
+        "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:
@@ -107,11 +126,12 @@ def redis_conn_with_in_progress_job_no_errors(redis_url, redis_ttl, job_id):#pyl
         cleanup_job(rconn, job_id, thejob)
 
 @pytest.fixture(scope="function")
-def redis_conn_with_in_progress_job_some_errors(redis_url, redis_ttl, job_id): # pylint: disable=[redefined-outer-name]
+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 = {
-        "job_id": job_id, "command": "some_test_command",
-        "ttl_seconds": redis_ttl, "job_type": "testjob", "extra_meta": {
+        "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(
@@ -124,11 +144,12 @@ def redis_conn_with_in_progress_job_some_errors(redis_url, redis_ttl, job_id): #
         cleanup_job(rconn, job_id, the_job)
 
 @pytest.fixture(scope="function")
-def redis_conn_with_completed_job_no_errors(redis_url, redis_ttl, job_id): # pylint: disable=[redefined-outer-name]
+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 = {
-        "job_id": job_id, "command": "some_test_command",
-        "ttl_seconds": redis_ttl, "job_type": "testjob", "extra_meta": {
+        "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:
@@ -137,11 +158,12 @@ def redis_conn_with_completed_job_no_errors(redis_url, redis_ttl, job_id): # pyl
         cleanup_job(rconn, job_id, the_job)
 
 @pytest.fixture(scope="function")
-def redis_conn_with_completed_job_some_errors(redis_url, redis_ttl, job_id): # pylint: disable=[redefined-outer-name]
+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 = {
-        "job_id": job_id, "command": "some_test_command",
-        "ttl_seconds": redis_ttl, "job_type": "testjob", "extra_meta": {
+        "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(
diff --git a/tests/qc_app/test_entry.py b/tests/qc_app/test_entry.py
index c0be26c..efc72a5 100644
--- a/tests/qc_app/test_entry.py
+++ b/tests/qc_app/test_entry.py
@@ -54,6 +54,7 @@ def test_post_with_correct_data(client):
     """
     response = client.post(
         "/", data={
+            "speciesid": 1,
             "filetype": "average",
             "qc_text_file": uploadable_file_object("no_data_errors.tsv")
         })
@@ -61,7 +62,7 @@ def test_post_with_correct_data(client):
     assert response.status_code == 302
     assert b'Redirecting...' in response.data
     assert (
-        b'/parse/parse?filename=no_data_errors.tsv&filetype=average'
+        b'/parse/parse?speciesid=1&filename=no_data_errors.tsv&filetype=average'
         in response.data)
 
 @pytest.mark.parametrize(
diff --git a/tests/qc_app/test_parse.py b/tests/qc_app/test_parse.py
index f173e0a..5e55688 100644
--- a/tests/qc_app/test_parse.py
+++ b/tests/qc_app/test_parse.py
@@ -4,11 +4,18 @@ import sys
 import redis
 import pytest
 
-from qc_app.jobs import job
+from qc_app.jobs import job, jobsnamespace
+
 from tests.conftest import uploadable_file_object
 
-def test_parse_with_existing_uploaded_file(
-        client, redis_url, job_id, monkeypatch):
+def test_parse_with_existing_uploaded_file(#pylint: disable=[too-many-arguments]
+        client,
+        db_url,
+        redis_url,
+        redis_ttl,
+        jobs_prefix,
+        job_id,
+        monkeypatch):
     """
     GIVEN: 1. A flask application testing client
            2. A valid file, and filetype
@@ -19,27 +26,30 @@ def test_parse_with_existing_uploaded_file(
     """
     monkeypatch.setattr("qc_app.jobs.uuid4", lambda : job_id)
     # Upload a file
+    speciesid = 1
     filename = "no_data_errors.tsv"
     filetype = "average"
     client.post(
         "/", data={
+            "speciesid": speciesid,
             "filetype": filetype,
             "qc_text_file": uploadable_file_object(filename)})
     # Checks
-    resp = client.get(f"/parse/parse?filename={filename}&filetype={filetype}")
+    resp = client.get(f"/parse/parse?speciesid={speciesid}&filename={filename}"
+                      f"&filetype={filetype}")
     assert resp.status_code == 302
     assert b'Redirecting...' in resp.data
     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, job_id)
+        the_job = job(rconn, jobsnamespace(), job_id)
 
-    assert the_job["job_id"] == job_id
+    assert the_job["jobid"] == job_id
     assert the_job["filename"] == filename
     assert the_job["command"] == " ".join([
-        sys.executable, "-m", "scripts.validate_file", filetype,
-        f"{client.application.config['UPLOAD_FOLDER']}/{filename}", redis_url,
-        job_id])
+        sys.executable, "-m", "scripts.validate_file", db_url, redis_url,
+        jobs_prefix, job_id, "--redisexpiry", str(redis_ttl), str(speciesid),
+        filetype, f"{client.application.config['UPLOAD_FOLDER']}/{filename}"])
 
 @pytest.mark.parametrize(
     "filename,uri,error_msgs",
diff --git a/tests/qc_app/test_uploads_with_zip_files.py b/tests/qc_app/test_uploads_with_zip_files.py
index 2a43a2d..fb101ad 100644
--- a/tests/qc_app/test_uploads_with_zip_files.py
+++ b/tests/qc_app/test_uploads_with_zip_files.py
@@ -36,12 +36,13 @@ def test_upload_zipfile_with_one_tsv_file(client):
     THEN: Ensure that the system redirects to the correct next URL
     """
     resp = client.post("/", data={
+        "speciesid": 1,
         "filetype": "average",
         "qc_text_file": uploadable_file_object("average.tsv.zip")})
     assert resp.status_code == 302
     assert b"Redirecting..." in resp.data
     assert (
-        b"/parse/parse?filename=average.tsv.zip&filetype=average"
+        b"/parse/parse?speciesid=1&filename=average.tsv.zip&filetype=average"
         in resp.data)
 
 def test_upload_zipfile_with_one_non_tsv_file(client):