Adds config and openwith tests.

test/data/MB266/VitessceConfig.json

@@ -1,6 +1,6 @@
 {
     "version": "1.0.16",
-    "name": "TestData",
+    "name": "TestDataset",
     "description": "Generated with omero-vitessce",
     "datasets": [
         {

test/integration/test_config.py

@@ -0,0 +1,133 @@
+"""Integration tests for index page."""
+import json
+import os
+import pytest
+
+from omeroweb.testlib import IWebTest  # , get
+# from django.urls import reverse
+from django.http.request import HttpRequest
+from django.http.request import QueryDict
+from omero.gateway import BlitzGateway
+
+from omero_vitessce import utils
+
+
+class TestConfig(IWebTest):
+    """Tests loading the index page."""
+    USER_NAME = "test_user"
+    USER_GROUP = "TestGroup"
+    USER_PWD = "password"
+
+    @pytest.fixture()
+    def conn(self):
+        """Set up a connection to the user/group holding the test data"""
+        client = IWebTest.new_client(self, group=TestConfig.USER_GROUP,
+                                     user=TestConfig.USER_NAME, perms=None,
+                                     owner=False, system=False, session=None,
+                                     password=TestConfig.USER_PWD, email=None,
+                                     privileges=None)
+        conn = BlitzGateway(client_obj=client)
+        return conn
+
+    def test_image_files(self, conn):
+        """Checks the retrieval of images and .csv attachements"""
+        i1_e = (set([]), set([]), set(["MB266-DAPI.tiff"]),
+                set(["http://localhost:4080/zarr/v0.4/image/1.zarr"]))
+        i2_e = (set([]), set([]), set(["MB266-CELLS.png"]),
+                set(["http://localhost:4080/zarr/v0.4/image/2.zarr"]))
+        d1_e = (set(["cells.csv", "embeddings.csv", "transcripts.csv",
+                     "feature_matrix.csv"]),
+                set(["http://localhost:4080/webclient/annotation/1",
+                     "http://localhost:4080/webclient/annotation/2",
+                     "http://localhost:4080/webclient/annotation/3",
+                     "http://localhost:4080/webclient/annotation/4"]),
+                set(["MB266-DAPI.tiff", "MB266-CELLS.png"]),
+                set(["http://localhost:4080/zarr/v0.4/image/1.zarr",
+                     "http://localhost:4080/zarr/v0.4/image/2.zarr"]))
+
+        i1_o = tuple(set(i) for i in utils.get_files_images("image", 1, conn))
+        i2_o = tuple(set(i) for i in utils.get_files_images("image", 2, conn))
+        d1_o = tuple(set(i) for i in utils.get_files_images("dataset",
+                                                            1, conn))
+
+        errors = []
+        if i1_o != i1_e:
+            errors.append(
+                    f"Wrong files found on image 1 {i1_o}, should be {i1_e}")
+        if i2_o != i2_e:
+            errors.append(
+                    f"Wrong files found on image 2 {i2_o}, should be {i2_e}")
+        if d1_o != d1_e:
+            errors.append(
+                    f"Wrong files found on dataset 1 {d1_o}, should be {d1_e}")
+        assert not errors, "errors occured:\n{}".format("\n".join(errors))
+
+    def test_config_files(self, conn):
+        """Checks the retrieval of .json config files"""
+        i1_e = (set([]), set([]))
+        i2_e = (set([]), set([]))
+        d1_e = (set(["VitessceConfig.json"]), set([
+            "http://localhost:4080/omero_vitessce/" +
+            "?config=http://localhost:4080/webclient/annotation/5"
+            ]))
+
+        i1_o = tuple(set(i) for i in utils.get_attached_configs("image",
+                                                                1, conn))
+        i2_o = tuple(set(i) for i in utils.get_attached_configs("image",
+                                                                2, conn))
+        d1_o = tuple(set(i) for i in utils.get_attached_configs("dataset",
+                                                                1, conn))
+
+        errors = []
+        if i1_o != i1_e:
+            errors.append(
+                    f"Wrong files found on image 1 {i1_o}, should be {i1_e}")
+        if i2_o != i2_e:
+            errors.append(
+                    f"Wrong files found on image 2 {i2_o}, should be {i2_e}")
+        if d1_o != d1_e:
+            errors.append(
+                    f"Wrong files found on dataset 1 {d1_o}, should be {d1_e}")
+        assert not errors, "errors occured:\n{}".format("\n".join(errors))
+
+    def test_config_file(self, conn):
+        """Test loading the app home page."""
+        json_path = os.path.join(os.environ["TARGET"],
+                                 "test/data/MB266/VitessceConfig.json")
+        with open(json_path) as jf:
+            expected_json = json.load(jf)
+        config_data = HttpRequest()
+        text = ("config_file_name=VitessceConfig.json&"
+                "images="
+                "http%3A%2F%2Flocalhost%3A4080%2F"
+                "zarr%2Fv0.4%2Fimage%2F1.zarr&"
+                "segmentation="
+                "http%3A%2F%2Flocalhost%3A4080%2F"
+                "zarr%2Fv0.4%2Fimage%2F2.zarr&"
+                "cell_identities="
+                "http%3A%2F%2Flocalhost%3A4080%2Fwebclient%2F"
+                "annotation%2F1&"
+                "cell_id_column=cell_id&"
+                "cell_label_column=label&"
+                "expression="
+                "http%3A%2F%2Flocalhost%3A4080%2Fwebclient%2F"
+                "annotation%2F4&"
+                "embeddings="
+                "http%3A%2F%2Flocalhost%3A4080%2Fwebclient%2F"
+                "annotation%2F2&"
+                "embedding_x=UMAP_1&"
+                "embedding_y=UMAP_2&"
+                "molecules="
+                "http%3A%2F%2Flocalhost%3A4080%2Fwebclient%2F"
+                "annotation%2F3&"
+                "molecule_id=id&"
+                "molecule_label=gene&"
+                "molecule_x=x&"
+                "molecule_y=y&"
+                "histograms=on&"
+                "heatmap=on&"
+                "status=on&"
+                "description=on")
+        config_data.POST = QueryDict(text)
+        vc = utils.create_config(config_data.POST, "dataset", 1, conn)
+        assert expected_json == vc.to_dict()

test/integration/test_pages.py

@@ -0,0 +1,31 @@
+"""Integration tests for all pages."""
+
+from omeroweb.testlib import IWebTest, get
+from django.urls import reverse
+
+
+class TestLoadPage(IWebTest):
+    """Tests loading the index page."""
+    USER_NAME = "test_user"
+    USER_GROUP = "TestGroup"
+    USER_PWD = "password"
+
+    def test_load_index(self):
+        """Test loading the app home page."""
+        django_client = self.new_django_client(TestLoadPage.USER_NAME,
+                                               TestLoadPage.USER_PWD)
+        index_url = reverse("vitessce_tab")
+        # asserts we get a 200 response code etc
+        rsp = get(django_client, index_url)
+        html_str = rsp.content.decode()
+        assert "React App" in html_str
+
+    def test_load_openwith(self):
+        """Test the openwith page."""
+        django_client = self.new_django_client(TestLoadPage.USER_NAME,
+                                               TestLoadPage.USER_PWD)
+        openwith_url = "http://localhost:4080/omero_vitessce/open/?image=1"
+        # asserts we get a 200 response code etc
+        rsp = get(django_client, openwith_url)
+        html_str = rsp.content.decode()
+        assert "There are no config files attached!" in html_str