fixing mock issues, adding random string to avoid dirname collisions

Author: bistline

ingest/dot_plot_genes.py

@@ -7,6 +7,8 @@
 import multiprocessing
 import sys
 import datetime
+import string
+import random
 from dateutil.relativedelta import relativedelta
 from functools import partial
 from bson.objectid import ObjectId
@@ -68,7 +70,9 @@ def __init__(
         self.mongo_connection = MongoConnection()
 
         # the cluster name here is not important, it is only used for directory names
-        self.cluster_name = f"cluster_entry_{self.cluster_group_id}"
+        # a random 6-letter slug is appended to the end to avoid directory collisions when running in CI
+        random_slug = ''.join(random.sample(string.ascii_letters, 6))
+        self.cluster_name = f"cluster_entry_{self.cluster_group_id}_{random_slug}"
         self.output_path = f"{self.cluster_name}/dot_plot_genes"
         self.exp_writer = ExpressionWriter(
             self.matrix_file_path, self.matrix_file_type, self.cluster_file, self.cluster_name, self.genes_path,

tests/test_dot_plot_genes.py

@@ -6,6 +6,7 @@
 import glob
 from shutil import rmtree
 from bson.objectid import ObjectId
+from unittest.mock import patch
 
 sys.path.append("../ingest")
 from dot_plot_genes import DotPlotGenes
@@ -210,7 +211,8 @@ def test_process_all_genes(self):
         rendered_gene = json.loads(gzip.open(rendered_path).read())
         self.assertEqual(self.SERGEF_METRICS, rendered_gene['exp_scores'])
 
-    def test_run_transform(self):
+    @patch("dot_plot_genes.bypass_mongo_writes", return_value=True)
+    def test_run_transform(self, mock_bypass):
         dot_plot = self.setup_sparse()
         dot_plot.transform()
         total_genes = os.listdir(f"{dot_plot.cluster_name}/dot_plot_genes")
@@ -219,3 +221,4 @@ def test_run_transform(self):
         self.assertTrue(os.path.exists(rendered_path))
         rendered_gene = json.loads(gzip.open(rendered_path).read())
         self.assertEqual(self.OXCT2_METRICS, rendered_gene['exp_scores'])
+        mock_bypass.assert_called_once()

tests/test_ingest.py

@@ -979,7 +979,8 @@ def test_execute_de_anndata(self):
             except:
                 print(f"Error while deleting file : {file}")
 
-    def test_ingest_dot_plot(self):
+    @patch("dot_plot_genes.bypass_mongo_writes", return_value=True)
+    def test_ingest_dot_plot(self, mock_bypass):
         args = [
             "--study-id",
             "5d276a50421aa9117c982845",
@@ -1006,6 +1007,7 @@ def test_ingest_dot_plot(self):
 
         self.assertEqual(len(status), 1)
         self.assertEqual(status[0], 0)
+        mock_bypass.assert_called_once()
 
     def test_get_action_from_args(self):
         args = [