add row link display override with assay comment (#1968)

CHANGELOG.rst

@@ -14,6 +14,7 @@ Added
 - **Samplesheets**
     - ``template_output_dir_display`` user setting (#1960)
     - Display BAM/CRAM/VCF omit patterns in study shortcut modal (#1963)
+    - Row links display override using assay comment (#1968)
 - **Taskflowbackend**
     - ``BatchCalculateChecksumTask`` retrying in case of timeouts (#1941)
 

docs_manual/source/metadata_advanced.rst

@@ -87,6 +87,18 @@ override the latter. Example:
     Study Assay File Name   a_assay.txt
     Comment[SODAR Assay Plugin] samplesheets_assay_generic_raw
 
+Similarly, you can override the assay table row link display with the comment
+``SODAR Assay Row Display``. Set it to "true" or "false" (or 1/0) to control
+whether row links should be displayed for this assay. Note that if you set this
+to true, the assay plugin used for the assay should implement the
+``get_row_path()`` method.
+
+.. code-block::
+
+    STUDY ASSAYS
+    Study Assay File Name   a_assay.txt
+    Comment[SODAR Assay Row Display] false
+
 SODAR currently supports the following assay plugins:
 
 - **DNA Sequencing**

docs_manual/source/sodar_release_notes.rst

@@ -14,6 +14,7 @@ v0.15.0 (WIP)
 Feature update.
 
 - Add BAM/CRAM/VCF omit pattern display in study shortcut modal
+- Add row links display override using assay comment
 - Add iRODS checksum calculation retrying
 - Add Cyberduck documentation
 - Disable lock requirement for project and role update taskflows

samplesheets/tests/test_views_ajax.py

@@ -61,6 +61,7 @@
     RENDER_HEIGHT_ROW,
     RENDER_HEIGHT_SCROLLBAR,
     STUDY_PLUGIN_NOT_FOUND_MSG,
+    ROW_LINK_DISPLAY_COMMENT,
 )
 
 
@@ -462,6 +463,26 @@ def test_get_inherited_owner(self):
         response_data = json.loads(response.data)
         self.assertEqual(response_data['perms']['edit_config'], True)
 
+    def test_get_display_row_links_override(self):
+        """Test GET with assay row link display override"""
+        self.assay.comments[ROW_LINK_DISPLAY_COMMENT] = 'false'
+        self.assay.save()
+        with self.login(self.user):
+            response = self.client.get(
+                reverse(
+                    'samplesheets:ajax_context',
+                    kwargs={'project': self.project.sodar_uuid},
+                )
+            )
+        self.assertEqual(response.status_code, 200)
+        response_data = json.loads(response.data)
+        # Initial value was True
+        self.assertFalse(
+            response_data['studies'][str(self.study.sodar_uuid)]['assays'][
+                str(self.assay.sodar_uuid)
+            ]['display_row_links']
+        )
+
 
 class TestStudyTablesAjaxView(IrodsAccessTicketMixin, SamplesheetsViewTestBase):
     """Tests for StudyTablesAjaxView"""

samplesheets/utils.py

@@ -375,3 +375,22 @@ def get_latest_file_path(paths):
     :param paths: List of strings
     """
     return sorted(paths, key=lambda x: x.split('/')[-1], reverse=True)[0]
+
+
+def get_bool(bool_string):
+    """
+    Return freeform string as boolean.
+
+    NOTE: Doing this as distutils is deprecated/removed..
+
+    :param bool_string: String
+    :raise: ValueError if value is not a string or can't be parsed
+    :return: bool
+    """
+    if not isinstance(bool_string, str):
+        raise ValueError('Value is not a string')
+    if bool_string.strip().lower() in ['1', 't', 'true', 'y', 'yes']:
+        return True
+    if bool_string.strip().lower() in ['0', 'f', 'false', 'n', 'no']:
+        return False
+    raise ValueError('Unable to parse value: {}'.format(bool_string))

samplesheets/views_ajax.py

@@ -45,6 +45,7 @@
     get_node_obj,
     get_webdav_url,
     get_ext_link_labels,
+    get_bool,
 )
 from samplesheets.views import (
     IrodsDataRequestModifyMixin,
@@ -86,6 +87,7 @@
 ERROR_NOT_FOUND = 'Collection not found'
 ERROR_NO_AUTH = 'User not authorized for iRODS collection'
 STUDY_PLUGIN_NOT_FOUND_MSG = 'Plugin not found for study'
+ROW_LINK_DISPLAY_COMMENT = 'SODAR Assay Row Display'
 
 
 # Base Ajax View Classes and Mixins --------------------------------------------
@@ -443,6 +445,24 @@ def get(self, request, *args, **kwargs):
             # Set up assay data
             for a in s.assays.all().order_by('pk'):
                 assay_plugin = a.get_plugin()
+                row_links = True
+                if ROW_LINK_DISPLAY_COMMENT in a.comments:
+                    try:
+                        row_links = get_bool(
+                            a.comments[ROW_LINK_DISPLAY_COMMENT]
+                        )
+                    except Exception as ex:
+                        logger.error(
+                            'Exception in retrieving row display comment "{}" '
+                            'for assay "{} ({})": {}'.format(
+                                ROW_LINK_DISPLAY_COMMENT,
+                                a.get_display_name(),
+                                a.sodar_uuid,
+                                ex,
+                            )
+                        )
+                elif assay_plugin:
+                    row_links = assay_plugin.display_row_links
                 ret_data['studies'][str(s.sodar_uuid)]['assays'][
                     str(a.sodar_uuid)
                 ] = {
@@ -451,9 +471,7 @@ def get(self, request, *args, **kwargs):
                     'irods_path': (
                         irods_backend.get_path(a) if irods_backend else None
                     ),
-                    'display_row_links': (
-                        assay_plugin.display_row_links if assay_plugin else True
-                    ),
+                    'display_row_links': row_links,
                     'plugin': assay_plugin.title if assay_plugin else None,
                 }