add assay plugin tests, fix and refactor (#1980, #2014, #2017)

CHANGELOG.rst

@@ -20,6 +20,8 @@ Added
 - **Samplesheets**
     - REST API list view pagination (#1994)
     - ``notify_email_irods_request`` user app setting (#1939)
+    - Assay app unit tests (#1980)
+    - Missing assay plugin ``__init__.py`` files (#2014)
 
 Changed
 -------
@@ -53,6 +55,7 @@ Fixed
 
 - **Samplesheets**
     - Timeline event status not updated in ``SheetDeleteVieW`` with iRODS collections enabled (#1798)
+    - Assay plugin ``update_row()`` setting links for empty file 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

@@ -0,0 +1,140 @@
+"""Plugin tests for the the cytof assay plugin"""
+
+import os
+
+from copy import deepcopy
+
+from samplesheets.assayapps.tests.base import AssayPluginTestBase
+from samplesheets.rendering import SIMPLE_LINK_TEMPLATE
+from samplesheets.views import MISC_FILES_COLL
+
+
+# Local constants
+ASSAY_NAME = 'testassayname'
+PANEL_NAME = 'testpanel'
+REPORT_NAME = 'report.txt'
+FILE_NAME = 'file1.txt'
+FILE_NAME2 = 'file2.txt'
+FILE_NAME3 = 'file3.txt'
+
+
+class TestCytofAssayPlugin(AssayPluginTestBase):
+    """Tests for cytof assay plugin"""
+
+    plugin_name = 'samplesheets_assay_cytof'
+    template_name = 'mass_cytometry'
+
+    def test_get_row_path_filled(self):
+        """Test get_row_path() with filled out assay name"""
+        self.assay_table['table_data'][0][20]['value'] = ASSAY_NAME
+        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, ASSAY_NAME)
+        self.assertEqual(row_path, expected)
+
+    def test_get_row_path_default(self):
+        """Test get_row_path() with default template values"""
+        # NOTE: Assay name is not filled by default, so we return None
+        row_path = self.plugin.get_row_path(
+            self.assay_table['table_data'][0],
+            self.assay_table,
+            self.assay,
+            self.assay_path,
+        )
+        self.assertEqual(row_path, None)
+
+    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
+        self.assay_table['table_data'][0][20]['value'] = ASSAY_NAME
+        self.assay_table['table_data'][0][26]['value'] = FILE_NAME
+        self.assay_table['table_data'][0][31]['value'] = FILE_NAME2
+        self.assay_table['table_data'][0][36]['value'] = FILE_NAME3
+        # Set expected data
+        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),
+        )
+        row_ex[26]['link'] = os.path.join(self.base_url, ASSAY_NAME, FILE_NAME)
+        row_ex[31]['link'] = os.path.join(self.base_url, ASSAY_NAME, FILE_NAME2)
+        row_ex[36]['link'] = os.path.join(self.base_url, ASSAY_NAME, FILE_NAME3)
+        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_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
+        self.assay_table['table_data'][0][26]['value'] = FILE_NAME
+        self.assay_table['table_data'][0][31]['value'] = FILE_NAME2
+        self.assay_table['table_data'][0][36]['value'] = FILE_NAME3
+        row_ex = deepcopy(self.assay_table['table_data'][0])
+        row_ex[16]['value'] = SIMPLE_LINK_TEMPLATE.format(
+            label=REPORT_NAME,
+            url=os.path.join(self.base_url, ASSAY_NAME, REPORT_NAME),
+        )
+        row_ex[26]['link'] = os.path.join(self.base_url, ASSAY_NAME, FILE_NAME)
+        row_ex[31]['link'] = os.path.join(self.base_url, ASSAY_NAME, FILE_NAME2)
+        row_ex[36]['link'] = os.path.join(self.base_url, ASSAY_NAME, FILE_NAME3)
+        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_barcode(self):
+        """Test update_row() with filled barcode key"""
+        # 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.assay_table['table_data'][0][26]['value'] = FILE_NAME
+        self.assay_table['table_data'][0][31]['value'] = FILE_NAME2
+        self.assay_table['table_data'][0][36]['value'] = FILE_NAME3
+        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),
+        )
+        row_ex[26]['link'] = os.path.join(self.base_url, ASSAY_NAME, FILE_NAME)
+        row_ex[31]['link'] = os.path.join(self.base_url, ASSAY_NAME, FILE_NAME2)
+        row_ex[36]['link'] = os.path.join(self.base_url, ASSAY_NAME, FILE_NAME3)
+        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_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"""
+        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)

samplesheets/assayapps/dna_sequencing/tests/test_plugins.py

@@ -0,0 +1,50 @@
+"""Plugin tests for the the dna_sequencing assay plugin"""
+
+import os
+
+from copy import deepcopy
+
+from samplesheets.assayapps.tests.base import AssayPluginTestBase
+
+
+# Local constants
+MATERIAL_NAME = 'alpha'
+MATERIAL_NAME_UPDATE = 'alpha-material-update'
+
+
+class TestDNASequencingAssayPlugin(AssayPluginTestBase):
+    """Tests for dna_sequencing assay plugin"""
+
+    plugin_name = 'samplesheets_assay_dna_sequencing'
+    template_name = 'generic'
+
+    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, MATERIAL_NAME)
+        self.assertEqual(row_path, expected)
+
+    def test_get_row_path_rename(self):
+        """Test get_row_path() with renamed material name"""
+        self.assay_table['table_data'][0][-1]['value'] = MATERIAL_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, MATERIAL_NAME_UPDATE)
+        self.assertEqual(row_path, expected)
+
+    def test_update_row(self):
+        """Test update_row()"""
+        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)

samplesheets/assayapps/generic/plugins.py

@@ -1,9 +1,11 @@
 """Assay app plugin for samplesheets"""
 
 import re
-from django.conf import settings
 
 from altamisa.constants import table_headers as th
+
+from django.conf import settings
+
 from samplesheets.plugins import SampleSheetAssayPluginPoint
 from samplesheets.rendering import SIMPLE_LINK_TEMPLATE
 from samplesheets.utils import get_top_header
@@ -16,6 +18,7 @@
 MISC_FILES_COMMENT = 'SODAR Assay Link MiscFiles'
 DATA_COMMENT_PREFIX = 'SODAR Assay Row Path'
 DATA_LINK_COMMENT = 'SODAR Assay Link Row'
+LINK_NAME_HEADERS = th.DATA_FILE_HEADERS + th.MATERIAL_NAME_HEADERS
 
 
 class SampleSheetAssayPlugin(SampleSheetAssayPluginPoint):
@@ -58,19 +61,11 @@ def _link_from_comment(cell, header, top_header, target_cols, url):
         :param target_cols: List of column names.
         :param url: Base URL for link target.
         """
-        # Do nothing if not string or link
-        if not isinstance(cell['value'], str) or re.search(
-            '.+ <.*>', cell['value']
-        ):
-            return True
-        # Special case for Material Names
+        # Special case for material names
         if (
-            (
-                top_header['value']
-                in th.DATA_FILE_HEADERS + th.MATERIAL_NAME_HEADERS
-            )
+            top_header['value'] in LINK_NAME_HEADERS
             and top_header['value'].lower() in target_cols
-            and (header['value'] == 'Name')
+            and (header['value'].lower() == 'name')
         ):
             cell['link'] = f"{url}/{cell['value']}"
             return True
@@ -81,6 +76,7 @@ def _link_from_comment(cell, header, top_header, target_cols, url):
                 url=f"{url}/{cell['value']}",
             )
             return True
+        return False
 
     @classmethod
     def _get_col_value(cls, target_col, row, table):
@@ -125,13 +121,11 @@ def get_row_path(self, row, table, assay, assay_path):
             for name, value in sorted(assay.comments.items())
             if name.startswith(DATA_COMMENT_PREFIX)
         ]
-
         data_collections = []
         for column_name in data_columns:
             col_value = self._get_col_value(column_name, row, table)
             if col_value:
                 data_collections.append(col_value)
-
         # Build iRODS path from list and stop at first None value
         if data_collections:
             data_path = '/' + '/'.join(data_collections)
@@ -167,7 +161,7 @@ def update_row(self, row, table, assay, index):
         data_cols = assay.comments.get(DATA_LINK_COMMENT)
         if data_cols:
             data_cols = data_cols.lower().split(';')
-            if table['irods_paths'][index]:
+            if 'irods_paths' in table and table['irods_paths'][index]:
                 row_path = table['irods_paths'][index]['path']
             else:
                 row_path = self.get_row_path(row, table, assay, assay_path)
@@ -177,29 +171,33 @@ def update_row(self, row, table, assay, index):
             if not top_header or i >= th_colspan:
                 top_header = get_top_header(table, i)
                 th_colspan += top_header['colspan']
-
+            # Skip if value is empty, not a string or already contains a link
+            if (
+                not row[i]['value']
+                or not isinstance(row[i]['value'], str)
+                or re.search('.+ <.*>', row[i]['value'])
+            ):
+                continue
             # TODO: Check if two comments reference the same column header?
-            # Create Results links
-            if results_cols:
-                if self._link_from_comment(
-                    row[i],
-                    header,
-                    top_header,
-                    results_cols,
-                    f'{base_url}/{RESULTS_COLL}',
-                ):
-                    continue
-            # Create MiscFiles links
-            if misc_cols:
-                if self._link_from_comment(
-                    row[i],
-                    header,
-                    top_header,
-                    misc_cols,
-                    f'{base_url}/{MISC_FILES_COLL}',
-                ):
-                    continue
-            # Create DataCollection links
+            # Create Results link
+            if results_cols and self._link_from_comment(
+                row[i],
+                header,
+                top_header,
+                results_cols,
+                f'{base_url}/{RESULTS_COLL}',
+            ):
+                continue
+            # Create MiscFiles link
+            if misc_cols and self._link_from_comment(
+                row[i],
+                header,
+                top_header,
+                misc_cols,
+                f'{base_url}/{MISC_FILES_COLL}',
+            ):
+                continue
+            # Create DataCollection link
             if data_cols:
                 self._link_from_comment(
                     row[i],