add microarray tests, refactor (#1980)

samplesheets/assayapps/cytof/tests/test_plugins.py

@@ -47,7 +47,7 @@ def test_get_row_path_default(self):
         )
         self.assertEqual(row_path, None)
 
-    def test_update_row_filled_panel(self):
+    def test_update_row_panel(self):
         """Test update_row() with filled panel name"""
         # Update unset values
         self.assay_table['table_data'][0][15]['value'] = PANEL_NAME
@@ -69,7 +69,7 @@ def test_update_row_filled_panel(self):
         )
         self.assertEqual(row, row_ex)
 
-    def test_update_row_filled_report(self):
+    def test_update_row_report(self):
         """Test update_row() with filled report file"""
         self.assay_table['table_data'][0][16]['value'] = REPORT_NAME
         self.assay_table['table_data'][0][20]['value'] = ASSAY_NAME
@@ -89,7 +89,7 @@ def test_update_row_filled_report(self):
         )
         self.assertEqual(row, row_ex)
 
-    def test_update_row_filled_barcode(self):
+    def test_update_row_barcode(self):
         """Test update_row() with filled barcode key"""
         # Rename header
         self.assay_table['field_header'][15]['value'] = 'Barcode Key'

samplesheets/assayapps/microarray/plugins.py

@@ -100,7 +100,6 @@ def get_row_path(self, row, table, assay, assay_path):
                     [assay_path, RAW_DATA_COLL, hybrid_name, scan_name]
                 )
                 return row_path
-
         return None
 
     def update_row(self, row, table, assay, index):
@@ -114,11 +113,7 @@ def update_row(self, row, table, assay, index):
         :return: List of dicts
         """
         assay_path = self.get_assay_path(assay)
-        if (
-            not settings.IRODS_WEBDAV_ENABLED
-            or not assay.study.investigation.irods_status
-            or not assay_path
-        ):
+        if not settings.IRODS_WEBDAV_ENABLED or not assay_path:
             return row
         row_path = self.get_row_path(row, table, assay, assay_path)
         if not row_path:
@@ -132,12 +127,8 @@ def update_row(self, row, table, assay, index):
                 and row[i]['value']
             ):
                 top_header = get_top_header(table, i)
-                if (
-                    top_header['value'].lower() in LINKED_FILES
-                    and row[i]['value']
-                ):
+                if top_header['value'].lower() in LINKED_FILES:
                     row[i]['link'] = base_url + '/' + row[i]['value']
-
         return row
 
     def update_cache(self, name=None, project=None, user=None):

samplesheets/assayapps/microarray/tests/test_plugins.py

@@ -0,0 +1,86 @@
+"""Plugin tests for the the microarray assay plugin"""
+
+import os
+
+from copy import deepcopy
+
+from django.conf import settings
+
+from samplesheets.assayapps.tests.base import AssayPluginTestBase
+
+
+# Local constants
+RAW_DATA_COLL = 'RawData'
+HYBRID_SCAN_NAME = 'alpha-S1-E1-H1'
+SCAN_NAME_UPDATE = 'alpha-S1-E1-scan-name'
+IMAGE_FILE = 'image.tiff'
+ARRAY_DATA_FILE = 'data.dat'
+MATRIX_FILE = "mat.rix"
+
+
+class TestMicroarrayAssayPlugin(AssayPluginTestBase):
+    """Tests for microarray assay plugin"""
+
+    plugin_name = 'samplesheets_assay_microarray'
+    template_name = 'microarray'
+
+    def test_get_row_path(self):
+        """Test get_row_path()"""
+        row_path = self.plugin.get_row_path(
+            self.assay_table['table_data'][0],
+            self.assay_table,
+            self.assay,
+            self.assay_path,
+        )
+        expected = os.path.join(
+            self.assay_path, RAW_DATA_COLL, HYBRID_SCAN_NAME, HYBRID_SCAN_NAME
+        )
+        self.assertEqual(row_path, expected)
+
+    def test_get_row_path_rename_scan(self):
+        """Test get_row_path() with renamed scan name"""
+        self.assay_table['table_data'][0][24]['value'] = SCAN_NAME_UPDATE
+        row_path = self.plugin.get_row_path(
+            self.assay_table['table_data'][0],
+            self.assay_table,
+            self.assay,
+            self.assay_path,
+        )
+        expected = os.path.join(
+            self.assay_path, RAW_DATA_COLL, HYBRID_SCAN_NAME, SCAN_NAME_UPDATE
+        )
+        self.assertEqual(row_path, expected)
+
+    def test_update_row_default(self):
+        """Test update_row() with default template values"""
+        row_ex = deepcopy(self.assay_table['table_data'][0])
+        row = self.plugin.update_row(
+            self.assay_table['table_data'][0], self.assay_table, self.assay, 0
+        )
+        self.assertEqual(row, row_ex)
+
+    def test_update_row_files(self):
+        """Test update_row() with filled file values"""
+        row_path = self.plugin.get_row_path(
+            self.assay_table['table_data'][0],
+            self.assay_table,
+            self.assay,
+            self.assay_path,
+        )
+        self.assay_table['table_data'][0][25]['value'] = IMAGE_FILE
+        self.assay_table['table_data'][0][26]['value'] = ARRAY_DATA_FILE
+        self.assay_table['table_data'][0][27]['value'] = MATRIX_FILE
+        row_ex = deepcopy(self.assay_table['table_data'][0])
+        row_ex[25]['link'] = settings.IRODS_WEBDAV_URL + os.path.join(
+            row_path, IMAGE_FILE
+        )
+        row_ex[26]['link'] = settings.IRODS_WEBDAV_URL + os.path.join(
+            row_path, ARRAY_DATA_FILE
+        )
+        row_ex[27]['link'] = settings.IRODS_WEBDAV_URL + os.path.join(
+            row_path, MATRIX_FILE
+        )
+        row = self.plugin.update_row(
+            self.assay_table['table_data'][0], self.assay_table, self.assay, 0
+        )
+        self.assertEqual(row, row_ex)