initial tests for cli utils

omics/cli/run_analyzer/utils.py

@@ -1,6 +1,6 @@
 import re
 
-ENGINES = ["WDL", "CWL", "Nextflow"]
+ENGINES = set(["WDL", "CWL", "NEXTFLOW"])
 
 _wdl_task_regex = r"^([^-]+)(-\d+-\d+.*)?$"
 _nextflow_task_regex = r"^(.+)(\s\(.+\))$"
@@ -22,7 +22,7 @@ def task_base_name(name: str, engine: str) -> str:
         if m:
             return m.group(1)
     # Nextflow
-    elif engine == "Nextflow":
+    elif engine == "NEXTFLOW":
         m = re.match(_nextflow_task_regex, name)
         if m:
             return m.group(1)
@@ -36,26 +36,30 @@ def task_base_name(name: str, engine: str) -> str:
     return name
 
 
+_sizes = {
+    "": 2,
+    "xlarge": 4,
+    "2xlarge": 8,
+    "4xlarge": 16,
+    "8xlarge": 32,
+    "12xlarge": 48,
+    "16xlarge": 64,
+    "24xlarge": 96,
+}
+_families = {"c": 2, "m": 4, "r": 8, "g4dn": 16, "g5": 16}
+
+
 def omics_instance_weight(instance: str) -> int:
     """Compute a numeric weight for an instance to be used in sorting or finding a max or min"""
-    sizes = {
-        "": 2,
-        "x": 4,
-        "2x": 8,
-        "4x": 16,
-        "8x": 32,
-        "12x": 48,
-        "16x": 64,
-        "24x": 96,
-    }
-    families = {"c": 2, "m": 4, "r": 8, "g4dn": 16, "g5": 16}
+    print(instance)
     # remove the "omics." from the string
-    instance.replace("omics.", "")
+    instance = instance.replace("omics.", "")
     # split the instance into family and size
     parts = instance.split(".")
+    print(parts)
     fam = parts[0]
-    size = parts[1] if len(parts) > 1 else ""
+    size = parts[1]
 
-    ccount = sizes[size]
-    weight = ccount * families[fam]
+    ccount = _sizes[size]
+    weight = ccount * _families[fam]
     return weight

tests/cli/run_analyzer/unit/test_utils.py

@@ -0,0 +1,37 @@
+import unittest
+
+import omics.cli.run_analyzer.utils as utils
+
+
+class TestRunAnalyzerUtils(unittest.TestCase):
+    def test_engine_names(self):
+        self.assertEqual(utils.ENGINES, set(["CWL", "WDL", "NEXTFLOW"]))
+
+    def test_task_base_name(self):
+        # CWL
+        self.assertEqual(utils.task_base_name("test", "CWL"), "test")
+        self.assertEqual(utils.task_base_name("test_1", "CWL"), "test")
+        self.assertEqual(utils.task_base_name("test_again_1", "CWL"), "test_again")
+        # WDL
+        self.assertEqual(utils.task_base_name("test", "WDL"), "test")
+        self.assertEqual(utils.task_base_name("test-01-1234", "WDL"), "test")
+        self.assertEqual(utils.task_base_name("test_again-10-2345", "WDL"), "test_again")
+        # Nextflow
+        self.assertEqual(utils.task_base_name("test", "NEXTFLOW"), "test")
+        self.assertEqual(utils.task_base_name("TEST:MODULE:FOO", "NEXTFLOW"), "TEST:MODULE:FOO")
+        self.assertEqual(
+            utils.task_base_name("TEST:MODULE:FOO (input1)", "NEXTFLOW"), "TEST:MODULE:FOO"
+        )
+
+    def test_task_base_name_invalid_engine(self):
+        self.assertRaises(ValueError, utils.task_base_name, "test", "INVALID")
+
+    def test_omics_instance_weight(self):
+        def _weight(instance):
+            return utils.omics_instance_weight(instance)
+
+        self.assertTrue(_weight("omics.c.2xlarge") < _weight("omics.c.4xlarge"))
+        self.assertTrue(_weight("omics.c.4xlarge") < _weight("omics.m.4xlarge"))
+        self.assertTrue(_weight("omics.m.4xlarge") < _weight("omics.r.4xlarge"))
+        self.assertTrue(_weight("omics.r.4xlarge") < _weight("omics.g4dn.4xlarge"))
+        self.assertTrue(_weight("omics.r.4xlarge") < _weight("omics.g5.4xlarge"))