refactor: use temporary directory (#25)

elixir-cloud-aai · Aug 7, 2024 · 467c3e8 · 467c3e8
1 parent fefefa3
commit 467c3e8
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Showing 3 changed files with 87 additions and 75 deletions.
diff --git a/.gitignore b/.gitignore
@@ -173,6 +173,4 @@ poetry.toml
 # LSP config files
 pyrightconfig.json
 
-# End of https://www.toptal.com/developers/gitignore/api/python
-
-outputs/
+# End of https://www.toptal.com/developers/gitignore/api/python
diff --git a/tests/tasks/task_bodies.py b/tests/tasks/task_bodies.py
@@ -4,9 +4,11 @@
 
 DIR = Path(__file__).parents[2]
 input_dir = DIR / "inputs"
-output_dir = DIR / "outputs"
 
-uppercase_task_body = {
+
+def get_uppercase_task_body(tmp_dir):
+    """Returns TES task body that makes the contents of a file uppercase."""
+    return {
         "name": "Hello world",
         "inputs": [
             {
@@ -22,7 +24,7 @@
         ],
         "outputs": [
             {
-                "url": f"file://{output_dir}/hello-upper.txt",
+                "url": f"file://{tmp_dir}/hello-upper.txt",
                 "path": "/outputs/hello-upper.txt",
                 "type": "FILE"
             }
@@ -40,7 +42,10 @@
         ]
     }
 
-decryption_task_body = {
+
+def get_decryption_task_body(tmp_dir):
+    """Returns TES task body that decrypts a crypt4GH file."""
+    return {
         "name": "Decrypt with secret key as environment variable",
         "inputs": [
             {
@@ -61,7 +66,7 @@
         ],
         "outputs": [
             {
-                "url": f"file://{output_dir}/hello-decrypted.txt",
+                "url": f"file://{tmp_dir}/hello-decrypted.txt",
                 "path": "/outputs/hello-decrypted.txt",
                 "type": "FILE"
             }
@@ -79,58 +84,61 @@
         ]
     }
 
-uppercase_task_with_decryption_body = {
-    "name": "Decrypt with secret key as environment variable",
-    "inputs": [
-        {
-            "url": f"file://{input_dir}/hello.c4gh",
-            "path": "/inputs/hello.c4gh",
-            "type": "FILE"
-        },
-        {
-            "url": f"file://{input_dir}/alice.sec",
-            "path": "/inputs/alice.sec",
-            "type": "FILE"
-        },
-        {
-            "url": f"file://{input_dir}/decrypt.sh",
-            "path": "/inputs/decrypt.sh",
-            "type": "FILE"
-        },
-        {
-            "url": f"file://{input_dir}/make_uppercase.py",
-            "path": "/inputs/make_uppercase.py",
-            "type": "FILE"
-        }
-    ],
-    "outputs": [
-        {
-            "url": f"file://{output_dir}/hello-upper-decrypt.txt",
-            "path": "/outputs/hello-upper-decrypt.txt",
-            "type": "FILE"
-        }
-    ],
-    "executors": [
-        {
-            "image": "athitheyag/c4gh:1.0",
-            "command": ["bash", "/inputs/decrypt.sh"],
-            "env": {
-                "INPUT_LOC": "/inputs/hello.c4gh",
-                "OUTPUT_LOC": "/vol/A/inputs/hello.txt",
-                "SECRET": "/inputs/alice.sec"
+
+def get_uppercase_task_with_decryption_body(tmp_dir):
+    """Returns TES task body that makes the contents of a crypt4GH file uppercase."""
+    return {
+        "name": "Decrypt with secret key as environment variable",
+        "inputs": [
+            {
+                "url": f"file://{input_dir}/hello.c4gh",
+                "path": "/inputs/hello.c4gh",
+                "type": "FILE"
+            },
+            {
+                "url": f"file://{input_dir}/alice.sec",
+                "path": "/inputs/alice.sec",
+                "type": "FILE"
+            },
+            {
+                "url": f"file://{input_dir}/decrypt.sh",
+                "path": "/inputs/decrypt.sh",
+                "type": "FILE"
+            },
+            {
+                "url": f"file://{input_dir}/make_uppercase.py",
+                "path": "/inputs/make_uppercase.py",
+                "type": "FILE"
             }
-        },
-        {
-            "image": "python:3",
-            "command": [
-                "python3",
-                "/inputs/make_uppercase.py",
-                "/vol/A/inputs/hello.txt"
-            ],
-            "stdout": "/outputs/hello-upper-decrypt.txt"
-        }
-    ],
-    "volumes": [
-        "/vol/A/inputs"
-    ]
+        ],
+        "outputs": [
+            {
+                "url": f"file://{tmp_dir}/hello-upper-decrypt.txt",
+                "path": "/outputs/hello-upper-decrypt.txt",
+                "type": "FILE"
+            }
+        ],
+        "executors": [
+            {
+                "image": "athitheyag/c4gh:1.0",
+                "command": ["bash", "/inputs/decrypt.sh"],
+                "env": {
+                    "INPUT_LOC": "/inputs/hello.c4gh",
+                    "OUTPUT_LOC": "/vol/A/inputs/hello.txt",
+                    "SECRET": "/inputs/alice.sec"
+                }
+            },
+            {
+                "image": "python:3",
+                "command": [
+                    "python3",
+                    "/inputs/make_uppercase.py",
+                    "/vol/A/inputs/hello.txt"
+                ],
+                "stdout": "/outputs/hello-upper-decrypt.txt"
+            }
+        ],
+        "volumes": [
+            "/vol/A/inputs"
+        ]
 }
diff --git a/tests/tasks/test_tasks.py b/tests/tasks/test_tasks.py
@@ -1,16 +1,17 @@
 """Tests for I/O and decryption tasks"""
 
 import json
+from pathlib import Path
+from tempfile import TemporaryDirectory
 from time import sleep
 
 import pytest
 import requests
 
 from task_bodies import (
-    output_dir,
-    uppercase_task_body,
-    decryption_task_body,
-    uppercase_task_with_decryption_body
+    get_decryption_task_body,
+    get_uppercase_task_body,
+    get_uppercase_task_with_decryption_body,
 )
 from tests.utils import timeout
 
@@ -20,17 +21,23 @@
 INPUT_TEXT = "hello world from the input!"
 
 
-def wait_for_file_download(filename):
+def wait_for_file_download(filename, output_path):
     """Waits for file with given filename to download."""
-    while not (output_dir/filename).exists():
+    while not (output_path/filename).exists():
         sleep(1)
 
 
+@pytest.fixture(name="output_dir")
+def fixture_output_dir():
+    """Returns temporary directory to store task outputs."""
+    return Path(TemporaryDirectory().name)
+
+
 @pytest.fixture(name="task")
-def fixture_task(request):
+def fixture_task(request, output_dir):
     """Returns response received after creating task."""
     return requests.post(
-        url=f"{TES_URL}/tasks", headers=HEADERS, json=request.param
+        url=f"{TES_URL}/tasks", headers=HEADERS, json=request.param(output_dir)
     )
 
 
@@ -54,17 +61,16 @@ def fixture_final_task_info(task):
 
 
 @pytest.mark.parametrize("task,filename,expected_output", [
-    (uppercase_task_body, "hello-upper.txt", INPUT_TEXT.upper()),
-    (decryption_task_body, "hello-decrypted.txt", INPUT_TEXT),
-    (uppercase_task_with_decryption_body, "hello-upper-decrypt.txt", INPUT_TEXT.upper())
+    (get_uppercase_task_body, "hello-upper.txt", INPUT_TEXT.upper()),
+    (get_decryption_task_body, "hello-decrypted.txt", INPUT_TEXT),
+    (get_uppercase_task_with_decryption_body, "hello-upper-decrypt.txt", INPUT_TEXT.upper())
 ], indirect=["task"])
 @timeout(time_limit=10)
-def test_task(task, final_task_info, filename, expected_output):  # pylint: disable=unused-argument
+def test_task(task, final_task_info, filename, expected_output, output_dir):  # pylint: disable=unused-argument
     """Test tasks for successful completion and intended behavior."""
     assert final_task_info["state"] == "COMPLETE"
 
-    wait_for_file_download(filename)
-
+    wait_for_file_download(filename=filename, output_path=output_dir)
     with open(output_dir/filename, encoding="utf-8") as f:
         output = f.read()
         assert output == expected_output