fix empty file name updating (#2017)

CHANGELOG.rst

@@ -55,6 +55,7 @@ Fixed
 
 - **Samplesheets**
     - Timeline event status not updated in ``SheetDeleteVieW`` with iRODS collections enabled (#1798)
+    - Assay plugin ``update_row()`` updating links for empty material names (#2017)
 
 Removed
 -------

samplesheets/assayapps/cytof/plugins.py

@@ -151,6 +151,8 @@ def update_row(self, row, table, assay, index):
                 and header['value'].lower() == 'name'
                 and top_header['value'].lower()
                 in ['raw data file', 'derived data file']
+                and row[i]['value']
+                and isinstance(row[i]['value'], str)
             ):
                 row[i]['link'] = (
                     base_url + '/' + mc_assay_name + '/' + row[i]['value']

samplesheets/assayapps/cytof/tests/test_plugins.py

@@ -111,7 +111,25 @@ def test_update_row_barcode(self):
         )
         self.assertEqual(row, row_ex)
 
-    # TODO: Test with empty file names after fixing #2017
+    def test_update_row_barcode_empty_file_names(self):
+        """Test update_row() with filled barcode key and empty file names"""
+        # Rename header
+        self.assay_table['field_header'][15]['value'] = 'Barcode Key'
+        self.assay_table['table_data'][0][15]['value'] = PANEL_NAME
+        self.assay_table['table_data'][0][20]['value'] = ASSAY_NAME
+        self.assertEqual(self.assay_table['table_data'][0][26]['value'], '')
+        self.assertEqual(self.assay_table['table_data'][0][31]['value'], '')
+        self.assertEqual(self.assay_table['table_data'][0][36]['value'], '')
+        row_ex = deepcopy(self.assay_table['table_data'][0])
+        row_ex[15]['value'] = SIMPLE_LINK_TEMPLATE.format(
+            label=PANEL_NAME,
+            url=os.path.join(self.base_url, MISC_FILES_COLL, PANEL_NAME),
+        )
+        # File names should not be updated
+        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_default(self):
         """Test update_row() with default template values"""

samplesheets/assayapps/generic_raw/plugins.py

@@ -83,6 +83,8 @@ def update_row(self, row, table, assay, index):
                 and header['item_type'] == 'DATA'
                 and header['value'].lower() == 'name'
                 and top_header['value'].lower() == 'raw data file'
+                and row[i]['value']
+                and isinstance(row[i]['value'], str)
             ):
                 row[i]['link'] = (
                     base_url + '/' + RAW_DATA_COLL + '/' + row[i]['value']

samplesheets/assayapps/generic_raw/tests/test_plugins.py

@@ -53,6 +53,16 @@ def test_update_row(self):
         )
         self.assertEqual(row, row_ex)
 
+    def test_update_row_empty_file_name(self):
+        """Test update_row() with empty file name"""
+        self.assay_table['top_header'][7]['value'] = 'Raw Data File'
+        self.assertEqual(self.assay_table['table_data'][0][44]['value'], '')
+        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_default(self):
         """Test update_row()"""
         row_ex = deepcopy(self.assay_table['table_data'][0])
@@ -61,8 +71,6 @@ def test_update_row_default(self):
         )
         self.assertEqual(row, row_ex)
 
-    # TODO: Test with empty file name for renamed field after fixing #2017
-
     def test_get_shortcuts(self):
         """Test get_shortcuts()"""
         expected = {

samplesheets/assayapps/meta_ms/plugins.py

@@ -96,6 +96,8 @@ def update_row(self, row, table, assay, index):
                 and header['value'].lower() == 'name'
                 and top_header['value'].lower()
                 in ['metabolite assignment file', 'raw spectral data file']
+                and row[i]['value']
+                and isinstance(row[i]['value'], str)
             ):
                 if top_header['value'].lower() == 'metabolite assignment file':
                     coll_name = MISC_FILES_COLL

samplesheets/assayapps/meta_ms/tests/test_plugins.py

@@ -54,7 +54,20 @@ def test_update_row(self):
         )
         self.assertEqual(row, row_ex)
 
-    # TODO: Test with empty file names after fixing #2017
+    def test_update_row_empty_file_names(self):
+        """Test update_row() with empty file names"""
+        self.assertEqual(self.assay_table['table_data'][0][44]['value'], '')
+        self.assertEqual(self.assay_table['table_data'][0][51]['value'], '')
+        self.assay_table['table_data'][0][55]['value'] = REPORT_NAME
+        row_ex = deepcopy(self.assay_table['table_data'][0])
+        row_ex[55]['value'] = SIMPLE_LINK_TEMPLATE.format(
+            label=REPORT_NAME,
+            url=os.path.join(self.base_url, RESULTS_COLL, REPORT_NAME),
+        )
+        row = self.plugin.update_row(
+            self.assay_table['table_data'][0], self.assay_table, self.assay, 0
+        )
+        self.assertEqual(row, row_ex)
 
     def test_get_shortcuts(self):
         """Test get_shortcuts()"""

samplesheets/assayapps/pep_ms/plugins.py

@@ -91,6 +91,8 @@ def update_row(self, row, table, assay, index):
                 header['obj_cls'] == 'GenericMaterial'
                 and header['item_type'] == 'DATA'
                 and header['value'].lower() == 'name'
+                and row[i]['value']
+                and isinstance(row[i]['value'], str)
             ):
                 # We assume all files to be in RawData
                 row[i]['link'] = (

samplesheets/assayapps/pep_ms/tests/test_plugins.py

@@ -54,7 +54,13 @@ def test_update_row(self):
         )
         self.assertEqual(row, row_ex)
 
-    # TODO: Test with empty file names after fixing #2017
+    def test_update_row_empty_file_names(self):
+        """Test update_row() with empty file names"""
+        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_get_shortcuts(self):
         """Test get_shortcuts()"""