add pep_ms tests, refactor (#1980)

samplesheets/assayapps/meta_ms/tests/test_plugins.py

@@ -4,13 +4,13 @@
 
 from copy import deepcopy
 
+from samplesheets.assayapps.meta_ms.plugins import RAW_DATA_COLL
 from samplesheets.assayapps.tests.base import AssayPluginTestBase
 from samplesheets.rendering import SIMPLE_LINK_TEMPLATE
 from samplesheets.views import MISC_FILES_COLL, RESULTS_COLL
 
 
 # Local constants
-RAW_DATA_COLL = 'RawData'
 REPORT_NAME = 'report.txt'
 FILE_NAME = 'file1.txt'
 FILE_NAME2 = 'file2.txt'

samplesheets/assayapps/microarray/tests/test_plugins.py

@@ -6,11 +6,11 @@
 
 from django.conf import settings
 
+from samplesheets.assayapps.microarray.plugins import RAW_DATA_COLL
 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'

samplesheets/assayapps/pep_ms/plugins.py

@@ -84,26 +84,8 @@ def update_row(self, row, table, assay, index):
             return row
         base_url = settings.IRODS_WEBDAV_URL + assay_path
 
-        # Check if MaxQuant is found
-        # NOTE: Currently disabled
-        '''
-        max_quant_found = False
-
-        for i in range(len(row)):
-            header = table['field_header'][i]
-
-            if (
-                header['obj_cls'] == 'Process'
-                and header['value'].lower() == 'analysis software name'
-                and row[i]['value'] == 'MaxQuant'
-            ):
-                max_quant_found = True
-                break
-        '''
-
         for i in range(len(row)):
             header = table['field_header'][i]
-
             # Data files
             if (
                 header['obj_cls'] == 'GenericMaterial'
@@ -114,20 +96,6 @@ def update_row(self, row, table, assay, index):
                 row[i]['link'] = (
                     base_url + '/' + RAW_DATA_COLL + '/' + row[i]['value']
                 )
-
-            # Process parameter files
-            # NOTE: Currently disabled
-            '''
-            elif (
-                max_quant_found
-                and header['obj_cls'] == 'Process'
-                and header['value'].lower() == 'analysis database file'
-            ):
-                row[i]['link'] = (
-                    base_url + '/' + MAX_QUANT_COLL + '/' + row[i]['value']
-                )
-            '''
-
         return row
 
     def get_shortcuts(self, assay):

samplesheets/assayapps/pep_ms/tests/test_plugins.py

@@ -0,0 +1,73 @@
+"""Plugin tests for the the pep_ms assay plugin"""
+
+import os
+
+from copy import deepcopy
+
+from samplesheets.assayapps.pep_ms.plugins import RAW_DATA_COLL, MAX_QUANT_COLL
+from samplesheets.assayapps.tests.base import AssayPluginTestBase
+from samplesheets.models import ISA_META_ASSAY_PLUGIN
+
+
+# Local constants
+PLUGIN_NAME = 'samplesheets_assay_pep_ms'
+FILE_NAME = 'file1.txt'
+FILE_NAME2 = 'file2.txt'
+
+
+class TestMetaMSAssayPlugin(AssayPluginTestBase):
+    """Tests for meta_ms assay plugin"""
+
+    plugin_name = PLUGIN_NAME
+    template_name = 'ms_meta_biocrates'
+
+    def setUp(self):
+        super().setUp()
+        # Override plugin
+        self.assay.comments[ISA_META_ASSAY_PLUGIN] = PLUGIN_NAME
+        self.assay.save()
+
+    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)
+        self.assertEqual(row_path, expected)
+
+    def test_update_row(self):
+        """Test update_row()"""
+        self.assay_table['table_data'][0][44]['value'] = FILE_NAME
+        self.assay_table['table_data'][0][51]['value'] = FILE_NAME2
+        row_ex = deepcopy(self.assay_table['table_data'][0])
+        row_ex[44]['link'] = os.path.join(
+            self.base_url, RAW_DATA_COLL, FILE_NAME
+        )
+        row_ex[51]['link'] = os.path.join(
+            self.base_url, RAW_DATA_COLL, FILE_NAME2
+        )
+        row = self.plugin.update_row(
+            self.assay_table['table_data'][0], self.assay_table, self.assay, 0
+        )
+        self.assertEqual(row, row_ex)
+
+    # TODO: Test with empty file names after fixing #2017
+
+    def test_get_shortcuts(self):
+        """Test get_shortcuts()"""
+        expected = [
+            {
+                'id': 'raw_data',
+                'label': 'Raw Data',
+                'path': os.path.join(self.assay_path, RAW_DATA_COLL),
+            },
+            {
+                'id': 'maxquant_results',
+                'label': 'MaxQuant Results',
+                'path': os.path.join(self.assay_path, MAX_QUANT_COLL),
+            },
+        ]
+        self.assertEqual(self.plugin.get_shortcuts(self.assay), expected)