test: speed up tests using fixture (#93)

Subset of HTS007 with single cell line for some tests, to increase
speed.
Also, replace use of pkg_resources with importlib.

thunorweb/tests/__init__.py

@@ -1,15 +1,14 @@
-import pkg_resources
+import importlib.resources
 import os
-import thunor
 
 
 def get_thunor_test_file(filename):
     try:
-        return pkg_resources.resource_stream('thunor', filename)
+        return importlib.resources.files('thunor').joinpath(filename)
     except OSError:
         # Provide a method to load from filesystem within Docker container
-        fn = os.path.join('thunor/thunor', filename)
+        fn = os.path.join('thunorcore/thunor', filename)
         if os.path.exists(fn) and os.path.isfile(fn):
-            return open(fn, 'rb')
+            return fn
 
         raise

thunorweb/tests/test_datasets.py

@@ -29,13 +29,10 @@ def setUpTestData(cls):
         dataset_id = resp_json['id']
         cls.d = HTSDataset.objects.get(pk=dataset_id)
 
-        hts007 = get_thunor_test_file('testdata/hts007.h5')
-        try:
+        with open(get_thunor_test_file('testdata/hts007.h5'), 'rb') as hts007:
             response = c.post(reverse('thunorweb:ajax_upload_platefiles'),
-                                  {'file_field[]': hts007, 'dataset_id':
-                                      cls.d.id})
-        finally:
-            hts007.close()
+                              {'file_field[]': hts007,
+                               'dataset_id': cls.d.id})
 
         assert response.status_code == HTTP_OK
         assert cls.d.plate_set.count() == 16

thunorweb/tests/test_plate_mapper.py

@@ -1,8 +1,5 @@
 from django.test import TestCase
-from django.core.files import File
-from thunorweb.plate_parsers import PlateFileParser
 from thunorweb.models import HTSDataset, CellLine, Drug
-from thunorweb.tests import get_thunor_test_file
 from django.contrib.auth import get_user_model
 from django.urls import reverse
 import json
@@ -12,24 +9,15 @@
 
 
 class TestPlateMapper(TestCase):
+    fixtures = ['testing-hts007-hcc1143.json']
+
     @classmethod
     def setUpTestData(cls):
         UserModel = get_user_model()
-        cls.user = UserModel.objects.create_user(
-            email='[email protected]', password='test')
-
-        cls.d = HTSDataset.objects.create(owner=cls.user, name='test')
-        hts007 = get_thunor_test_file('testdata/hts007.h5')
-        try:
-            f = File(hts007, name='hts007.h5')
-            pfp = PlateFileParser(f, dataset=cls.d)
-            results = pfp.parse_all()
-        finally:
-            hts007.close()
-
-        assert len(results) == 1
-        assert results[0]['success']
-        assert results[0]['file_format'] == 'HDF5'
+        cls.user = UserModel.objects.get(
+            email='[email protected]')
+
+        cls.d = HTSDataset.objects.get(owner=cls.user, name='test')
 
     def test_load_save_plate(self):
         plate_id = self.d.plate_set.first().id

thunorweb/tests/test_plate_parsers.py

@@ -17,18 +17,14 @@ def setUpTestData(cls):
     # HDF parsing is tested elsewhere
 
     def test_parse_vanderbilt_csv(self):
-        hts007 = get_thunor_test_file('testdata/hts007.h5')
-
         with io.StringIO() as csv_buffer:
             # convert HDF to CSV in memory
-            try:
+            with open(get_thunor_test_file('testdata/hts007.h5'), 'rb') as hts007:
                 thunor.io.write_vanderbilt_hts(
                     df_data=thunor.io.read_hdf(hts007),
                     filename=csv_buffer,
                     sep=','
                 )
-            finally:
-                hts007.close()
 
             csv_buffer.seek(0)
 
@@ -41,12 +37,10 @@ def test_parse_vanderbilt_csv(self):
         assert results[0]['file_format'] == 'Vanderbilt HTS Core'
 
     def test_parse_incucyte(self):
-        testfile = get_thunor_test_file('testdata/test_incucyte_minimal.txt')
-
-        try:
+        with open(get_thunor_test_file('testdata/test_incucyte_minimal.txt'),
+                  'rb') as testfile:
             filedata = io.BytesIO(testfile.read())
-        finally:
-            testfile.close()
+
         pfp = PlateFileParser(File(filedata, name='test.txt'),
                               dataset=self.d)
         results = pfp.parse_all()

thunorweb/tests/test_plots.py

@@ -11,31 +11,20 @@
 
 
 class TestPlots(TestCase):
+    fixtures = ['testing-hts007-hcc1143.json']
+
     @classmethod
     def setUpTestData(cls):
         UserModel = get_user_model()
-        cls.user = UserModel.objects.create_user(
-            email='[email protected]', password='test')
+        cls.user = UserModel.objects.get(
+            email='[email protected]')
         cls.other_user = UserModel.objects.create_user(
             email='[email protected]', password='test')
+
         c = Client()
         c.force_login(cls.user)
 
-        resp = c.post(reverse('thunorweb:ajax_create_dataset'),
-                      {'name': 'test'})
-        resp_json = json.loads(resp.content)
-        dataset_id = resp_json['id']
-        cls.d = HTSDataset.objects.get(pk=dataset_id)
-
-        hts007 = get_thunor_test_file('testdata/hts007.h5')
-        try:
-            response = c.post(reverse('thunorweb:ajax_upload_platefiles'),
-                                  {'file_field[]': hts007, 'dataset_id':
-                                      cls.d.id})
-        finally:
-            hts007.close()
-
-        assert response.status_code == HTTP_OK
+        cls.d = HTSDataset.objects.get()
 
         # Create some cell line and drug tags
         entities_per_tag = 3
@@ -58,7 +47,7 @@ def setUpTestData(cls):
         for tag_num in range(num_tags):
             idx = range(tag_num * entities_per_tag,
                         tag_num * (entities_per_tag + 1))
-            cltags[tag_num].cell_lines.set([cell_lines[i] for i in idx])
+            cltags[tag_num].cell_lines.set([cell_lines[0]])
             drtags[tag_num].drugs.set([drugs[i] for i in idx])
 
         # Get the dataset groupings