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authorBonfaceKilz2021-02-12 21:12:47 +0300
committerBonfaceKilz2021-02-12 21:13:30 +0300
commit9d5908f8fbf6e9f0b4f4567f61098653109c436c (patch)
treed1c4f9fb465a74402230ed6ffd78957a8fe24aea
parentf887baaf66cc157f0c77237c41e70e42fe03549c (diff)
downloadgenenetwork3-9d5908f8fbf6e9f0b4f4567f61098653109c436c.tar.gz
Add new procedure for queueing a command
* gn3/commands.py (queue_cmd): New procedure. * tests/unit/test_commands.py: New test-cases for ^^.
-rw-r--r--gn3/commands.py29
-rw-r--r--tests/unit/test_commands.py43
2 files changed, 72 insertions, 0 deletions
diff --git a/gn3/commands.py b/gn3/commands.py
index 50b6d29..9692f62 100644
--- a/gn3/commands.py
+++ b/gn3/commands.py
@@ -1,9 +1,13 @@
"""Procedures used to work with the various bio-informatics cli
commands"""
+from datetime import datetime
from typing import Dict
from typing import List
from typing import Optional
+from uuid import uuid4
+from redis.client import Redis # Used only in type hinting
+from gn3.exceptions import RedisConnectionError
from gn3.file_utils import lookup_file
from gn3.file_utils import jsonfile_to_dict
@@ -40,3 +44,28 @@ def compose_gemma_cmd(
cmd += (" "
" ".join([f" {arg}" for arg in gemma_args]))
return cmd
+
+
+def queue_cmd(cmd: str, conn: Redis) -> str:
+ """Given a command CMD, and a redis connection CONN, queue it in Redis
+with an initial status of 'queued'. The following status codes are
+supported:
+
+ queued: Unprocessed; Still in the queue
+ running: Still running
+ success: Successful completion
+ error: Erroneous completion
+
+ """
+ if not conn.ping():
+ raise RedisConnectionError
+ unique_id = ("cmd::"
+ f"{datetime.now().strftime('%Y-%m-%d%H-%M%S-%M%S-')}"
+ f"{str(uuid4())}")
+ for key, value in {"cmd": cmd,
+ "result": "",
+ "status": "queued"}.items():
+ conn.hset(key, value, unique_id)
+ conn.rpush("GN2::job-queue",
+ unique_id)
+ return unique_id
diff --git a/tests/unit/test_commands.py b/tests/unit/test_commands.py
index a319332..a1ac6eb 100644
--- a/tests/unit/test_commands.py
+++ b/tests/unit/test_commands.py
@@ -2,8 +2,21 @@
import os
import unittest
+from dataclasses import dataclass
+from datetime import datetime
+from typing import Callable
from unittest import mock
from gn3.commands import compose_gemma_cmd
+from gn3.commands import queue_cmd
+from gn3.exceptions import RedisConnectionError
+
+
+@dataclass
+class MockRedis:
+ """Mock Redis connection"""
+ ping: Callable
+ hset: mock.MagicMock
+ rpush: mock.MagicMock
class TestCommands(unittest.TestCase):
@@ -27,3 +40,33 @@ class TestCommands(unittest.TestCase):
"-g /tmp/genofile.txt "
"-p /tmp/gf13Ad0tRX/phenofile.txt"
" -gk"))
+
+ def test_queue_cmd_exception_raised_when_redis_is_down(self):
+ """Test that the correct error is raised when Redis is unavailable"""
+ self.assertRaises(RedisConnectionError,
+ queue_cmd,
+ "ls",
+ MockRedis(ping=lambda: False,
+ hset=mock.MagicMock(),
+ rpush=mock.MagicMock()))
+
+ @mock.patch("gn3.commands.datetime")
+ @mock.patch("gn3.commands.uuid4")
+ def test_queue_cmd_right_correct_calls_to_redis(self, mock_uuid4,
+ mock_datetime):
+ """Test that the cmd is queued properly"""
+ mock_uuid4.return_value = 1234
+ mock_datetime.now.return_value = datetime.fromisoformat('2021-02-12 '
+ '17:32:24.'
+ '859097')
+ mock_redis_conn = MockRedis(ping=lambda: True,
+ hset=mock.MagicMock(),
+ rpush=mock.MagicMock())
+ actual_unique_id = "cmd::2021-02-1217-3224-3224-1234"
+ self.assertEqual(queue_cmd("ls", mock_redis_conn), actual_unique_id)
+ mock_redis_conn.hset.assert_has_calls(
+ [mock.call("cmd", "ls", actual_unique_id),
+ mock.call("result", "", actual_unique_id),
+ mock.call("status", "queued", actual_unique_id)])
+ mock_redis_conn.rpush.assert_has_calls(
+ [mock.call("GN2::job-queue", actual_unique_id)])