init pytests

.github/workflows/pip.yml → .github/workflows/pytest.yml

@@ -1,4 +1,4 @@
-name: install
+name: test
 on: [push, pull_request]
 jobs:
   pip:
@@ -9,4 +9,6 @@ jobs:
       with:
         python-version: '3.12'
         cache: 'pip'
-    - run: pip install .
+    - run: | 
+      pip install .
+      pytest

pyproject.toml

@@ -28,7 +28,8 @@ dependencies = [
   "pyyaml >= 6.0",
   "rich_click >= 1.8.3",
   "dominate >= 2.9.1",
-  "tabulate >= 0.9.0"
+  "tabulate >= 0.9.0",
+  "pytest >= 8.2.2"
 ]
 
 [project.scripts]

tests/test_findFinishedFlowCells.py

@@ -0,0 +1,60 @@
+from pathlib import Path
+import pytest
+import configparser
+import urllib3
+from BRB.findFinishedFlowCells import flowCellProcessed, markFinished, queryParkour
+
+
+@pytest.fixture(scope='session')
+def ifs(tmp_path_factory):
+  fp = tmp_path_factory.mktemp("flowcells")
+  Path(fp,"fc_fin").mkdir()
+  Path(fp, "fc_fin", "analysis.done").touch()
+  Path(fp,"fc_unfin").mkdir()
+  return fp
+
+
+def create_conf(l = []):
+    '''
+    sets up a config, where every list (_l) in l gets set in config as :
+    config[_l[0]] = {_l[1]: _l[2]}
+    
+    Additionaly some garbage values for parkour API gets set
+    '''
+    config = configparser.ConfigParser()
+    config['Parkour'] = {
+        "QueryURL": "https://parkour-demo.ie-freiburg.mpg.de/nonext_api",
+        "user": "jefke",
+        "password": "123",
+        "cert": ""
+    }
+    config['Options'] = {'runID': '150416_SN7001180_0196_BC605HACXX'}
+    for _l in l:
+        config[_l[0]] = {_l[1]: _l[2]}
+    return config
+
+class TestfindFinishedFlowCells:
+    def test_flowCellProcessed(self, ifs):
+        config = create_conf([
+            ['Paths', 'baseData', ifs],
+            ['Options', 'runID', 'fc_fin']
+        ])
+        assert flowCellProcessed(config) == True
+        config = create_conf([
+            ['Paths', 'baseData', ifs],
+            ['Options', 'runID', 'fc_unfin']
+        ])
+        assert flowCellProcessed(config) == False
+
+    def test_markFinished(self, ifs):
+        config = create_conf([
+            ['Paths', 'baseData', ifs],
+            ['Options', 'runID', 'fc_unfin'],
+        ])
+        markFinished(config)
+        assert Path(ifs, 'fc_unfin', 'analysis.done').exists()
+
+    def test_queryParkour(self):
+        urllib3.disable_warnings(urllib3.exceptions.InsecureRequestWarning)
+        config = create_conf()
+        assert len(queryParkour(config)) == 0